Fix HISAT2 strandedness parameter

tools/hisat2/hisat2_macros.xml

@@ -1,148 +1,30 @@
-<?xml version="1.0"?>
 <macros>
-    <xml name="single_paired_selector">
-        <param name="paired_selector" type="select" label="Single end or paired reads?">
-            <option value="paired">Paired reads</option>
-            <option value="single">Unpaired reads</option>
+    <xml name="paired_end_options">
+
+        <param name="rna_strandness" argument="--rna-strandness" type="select" label="Specify strand information"
+                help="'FR' means a read corresponds to a transcript. 'RF' means a read corresponds to the reverse complemented counterpart of a transcript. With this option being used, every read alignment will have an XS attribute tag: '+' means a read belongs to a transcript on '+' strand of genome. '-' means a read belongs to a transcript on '-' strand of genome.">
+                <option value="">Unstranded</option>
+                <option value="FR">Forward (FR)</option>
+                <option value="RF">Reverse (RF)</option>
         </param>
-    </xml>
-    <xml name="paired_input_conditional" tokens="ftype">
-        <conditional name="paired">
-            <expand macro="single_paired_selector" />
-            <when value="paired">
-                <conditional name="collection" label="Data structure">
-                    <param name="collection_selector" type="select" label="Input is structured as" help="If a list of pairs is selected, HISAT2 will run in batch mode over each pair in the list, producing a list of output bam files">
-                        <option value="files">Individual files</option>
-                        <option value="collection">Pair collection or list of pairs</option>
-                    </param>
-                    <when value="collection">
-                        <param name="reads" type="data_collection" collection_type="paired" format="@FTYPE@" label="Paired reads" />
-                    </when>
-                    <when value="files">
-                        <param name="forward" type="data" format="@FTYPE@" label="Forward reads" />
-                        <param name="reverse" type="data" format="@FTYPE@" label="Reverse reads" />
-                    </when>
-                </conditional>
-                <expand macro="paired_end_conditional" />
-                <expand macro="paired_end_output" />
-            </when>
-            <when value="single">
-                <param name="reads" type="data" format="@FTYPE@" label="Reads" />
-                <param name="unaligned_file" argument="--un-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" />
-                <param name="aligned_file" argument="--al-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" />
-            </when>
-        </conditional>
-    </xml>
-    <xml name="paired_end_conditional">
-        <conditional name="paired_end_options">
-            <param name="paired_end_options_selector" type="select" label="Paired-end options">
+
+        <conditional name="paired_options">
+            <param name="paired_options_selector" type="select" label="Paired-end options" help="See &quot;Alignment Options&quot; section of Help below for information">
                 <option value="defaults">Use default values</option>
                 <option value="advanced">Specify paired-end parameters</option>
             </param>
-            <when value="defaults" />
+            <when value="defaults"/>
             <when value="advanced">
-                <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" label="Disable alignments of individual mates" help="By default, when hisat cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates. This option disables that behavior" />
-                <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" label="Disable alignments of individual mates" help="By default, hisat looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior" />
-                <param name="skip_reverse" type="boolean" truevalue="--norc" falsevalue="" label="Skip reference strand of reference" help="If --norc is specified, hisat will not attempt to align unpaired reads against the reverse-complement (Crick) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes hisat to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand" />
+                <param name="fr_rf_ff" argument="--fr/--rf/--ff" type="select" display="radio" label="Select the upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand"
+                       help="E.g., if `--fr` is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (`-I` and `-X`) are met, that alignment is valid.  Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. `--rf` likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. `--ff` requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented; Default=--fr (appropriate for Illumina's Paired-end Sequencing Assay)">
+                    <option value="--fr" selected="True">--fr</option>
+                    <option value="--rf">--rf</option>
+                    <option value="--ff">--ff</option>
+                </param>
+                <param argument="--no-mixed" name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="By default, when `hisat2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default: False"/>
+                <param argument="--no-discordant" name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `hisat2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default: False"/>
             </when>
         </conditional>
-    </xml>
-    <xml name="paired_end_output">
-        <param name="unaligned_file" argument="--un-conc-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" />
-        <param name="aligned_file" argument="--al-conc-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" />
-    </xml>
-    <token name="@paired_end_options@">
-        #if str( $input_format.paired.unaligned_file ) == "true":
-            #if $compressed == "GZ":
-                --un-conc-gz '${output_unaligned_reads_l}'
-            #else if $compressed == "BZ2":
-                --un-conc-bz2 '${output_unaligned_reads_l}'
-            #else:
-                --un-conc '${output_unaligned_reads_l}'
-            #end if
-        #end if
-        #if str( $input_format.paired.aligned_file ) == "true":
-            #if $compressed == "GZ":
-                --al-conc-gz '${output_aligned_reads_l}'
-            #else if $compressed == "BZ2"
-                --al-conc-bz2 '${output_aligned_reads_l}'
-            #else:
-                --al-conc '${output_aligned_reads_l}'
-            #end if
-        #end if
-        #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced':
-            ${input_format.paired.paired_end_options.no_mixed}
-            ${input_format.paired.paired_end_options.no_discordant}
-        #end if
-    </token>
-    <token name="@strandedness_parameters@">
-        #if str($spliced_options.spliced_options_selector) == "advanced":
-            #if str($spliced_options.rna_strandness).strip() != '':
-                --rna-strandness $spliced_options.rna_strandness
-            #end if
-        #end if
-    </token>
-    <token name="@FASTQGZ_SETUP@">
-<![CDATA[
-        #set compressed="False"
-        #if str($input_format.paired.paired_selector) == 'paired':
-            #if str($input_format.paired.collection.collection_selector) == 'collection':
-                #if $input_format.paired.collection.reads.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
-                    #set read1 = "input_f.fastq.gz"
-                    #set compressed = "GZ"
-                #else if $input_format.paired.collection.reads.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-                    #set read1 = "input_f.fastq.bz2"
-                    #set compressed = "BZ2"
-                #else:
-                    #set read1 = "input_f.fastq"
-                #end if
-                ln -f -s '${input_format.paired.collection.reads.forward}' ${read1} &&
 
-                #if $input_format.paired.collection.reads.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
-                    #set read2 = "input_r.fastq.gz"
-                    #set compressed = "GZ"
-                #else if $input_format.paired.collection.reads.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-                    #set read2 = "input_r.fastq.bz2"
-                    #set compressed = "BZ2"
-                #else:
-                    #set read2 = "input_r.fastq"
-                #end if
-                ln -f -s '${input_format.paired.collection.reads.reverse}' ${read2} &&
-            #else:
-                #if $input_format.paired.collection.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
-                    #set read1 = "input_f.fastq.gz"
-                    #set compressed = "GZ"
-                #else if $input_format.paired.collection.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-                    #set read1 = "input_f.fastq.bz2"
-                    #set compressed = "BZ2"
-                #else:
-                    #set read1 = "input_f.fastq"
-                #end if
-                ln -f -s '${input_format.paired.collection.forward}' ${read1} &&
-
-                #if $input_format.paired.collection.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
-                    #set read2 = "input_r.fastq.gz"
-                    #set compressed = "GZ"
-                #else if $input_format.paired.collection.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-                    #set read2 = "input_r.fastq.bz2"
-                    #set compressed = "BZ2"
-                #else:
-                    #set read2 = "input_r.fastq"
-                #end if
-                ln -f -s '${input_format.paired.collection.reverse}' ${read2} &&
-            #end if
-        #else:
-            #if $input_format.paired.reads.is_of_type("fastq.gz", "fastqsanger.gz"):
-                #set read1 = "input_f.fastq.gz"
-                #set compressed = "GZ"
-            #else if $input_format.paired.reads.is_of_type("fastq.bz2", "fastqsanger.bz2"):
-                #set read1 = "input_f.fastq.bz2"
-                #set compressed = "BZ2"
-            #else:
-                #set read1 = "input_f.fastq"
-            #end if
-            ln -s '${input_format.paired.reads}' ${read1} &&
-        #end if
-]]>
-    </token>
-</macros>
+    </xml>
+</macros>

tools/hisat2/test-data/cached_locally/hisat2_indexes.loc

@@ -0,0 +1 @@
+phiX	phiX	PhiX	${__HERE__}/phiX

tools/hisat2/test-data/cached_locally/phiX.fa

@@ -0,0 +1,79 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
+

tools/hisat2/test-data/hisat_output.summary

@@ -0,0 +1,6 @@
+HISAT2 summary stats:
+	Total reads: 10
+		Aligned 0 time: 0 (0.00%)
+		Aligned 1 time: 10 (100.00%)
+		Aligned >1 times: 0 (0.00%)
+	Overall alignment rate: 100.00%

tools/hisat2/tool_data_table_conf.xml.test

@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of indexes in the HISAT mapper format -->
+    <table name="hisat2_indexes" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/cached_locally/hisat2_indexes.loc" />
+    </table>
+</tables>