chira: fix parameters

tools/chira/chira_collapse.xml

@@ -1,9 +1,9 @@
-<tool id="chira_collapse" name="ChiRA collapse" version="@WRAPPER_VERSION@1">
+<tool id="chira_collapse" name="ChiRA collapse" version="@TOOL_VERSION@1">
     <description>deduplicate fastq reads</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />    
     <command><![CDATA[
         chira_collapse.py

tools/chira/chira_extract.xml

@@ -1,9 +1,9 @@
-<tool id="chira_extract" name="ChiRA extract" version="@WRAPPER_VERSION@0">
+<tool id="chira_extract" name="ChiRA extract" version="@TOOL_VERSION@1">
     <description>extrat the chimeras</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command detect_errors="aggressive"><![CDATA[
         #set $genomic_fasta = ''
@@ -17,16 +17,16 @@
             #end if
         #end if
         chira_extract.py
-        -l '$loci'
+        --loci '$loci'
         #if str($annotation.annot_choice) == "yes":
-            -g '$annotation.gtf'
+            --gtf '$annotation.gtf'
             #if $hybridize:
-                -f '$genomic_fasta'
+                --ref '$genomic_fasta'
             #end if
         #end if
-        -tc '$tpm_cutoff'
-        -sc '$score_cutoff'
-        -co '$chimeric_overlap'
+        --tpm_cutoff '$tpm_cutoff'
+        --score_cutoff '$score_cutoff'
+        --chimeric_overlap '$chimeric_overlap'
         #if str($reference.ref_type) == "single":
             -f1 '$reference.ref_fasta'
         #else if str($reference.ref_type) == "split":
@@ -35,91 +35,92 @@
         #end if
         $hybridize
         $seed_interaction
-        -sbp '$seed_bp'
-        -smpu '$seed_min_pu'
-        -acc '$accessibility'
-        -accw '$acc_width'
-        -m '$intarna_mode'
+        --seed_bp '$seed_bp'
+        --seed_min_pu '$seed_min_pu'
+        --accessibility '$accessibility'
+        --acc_width '$acc_width'
+        --intarna_mode '$intarna_mode'
+        --temperature $temperature
         $summarize
-        -p "\${GALAXY_SLOTS:-2}"
-        -o ./
+        --processes "\${GALAXY_SLOTS:-2}"
+        --out ./
     ]]></command>
 
     <inputs>
-        <param format="tabular" name="loci" type="data" label="File containing CRLs information"/>
+        <param format="tabular" argument="--loci" type="data" label="File containing CRLs information"/>
         <conditional name="annotation">
             <param name="annot_choice" type="select" label="Have genomic information?"
                    help="Selecet Yes if you have an annotation file and provide corresponding genomic fasta file">
                 <option value="yes">Yes</option>
                 <option value="no">No</option>
             </param>
             <when value="yes">
-                <param format="gtf,gff" name="gtf" type="data" label="Annotations in GTF format"/>
+                <param format="gtf,gff" argument="--gtf" type="data" label="Annotations in GTF format"/>
                 <conditional name="fasta_source">
                     <param name="fasta_source_selector" type="select" label="Choose the source for the FASTA file">
                         <option value="history" selected="true">History</option>
                         <option value="preloaded">Server indexed files</option>
                     </param>
                     <when value="history">
-                        <param name="fasta" type="data" format="fasta" label="Genomic FASTA file" />
+                        <param argument="--ref" name="fasta" type="data" format="fasta" label="Genomic FASTA file" />
                     </when>
                     <when value="preloaded">
-                       <param name="fasta_id" type="select" label="Select FASTA index">
-                          <options from_data_table="fasta_indexes" />
-                       </param>
+                        <param argument="--ref" name="fasta_id" type="select" label="Select FASTA index">
+                            <options from_data_table="fasta_indexes" />
+                        </param>
                     </when>
                 </conditional>
             </when>
             <when value="no">
                 <!-- Do nothing -->
             </when>
         </conditional>
-        <param name="tpm_cutoff" type="float" value="0" label="TPM cut-off" min="0" max="1"
+        <param argument="--tpm_cutoff" type="float" value="0" label="TPM cut-off" min="0" max="1"
                help="Transcripts with less than this percentile TPMs will be discarded in the final output. [0-1.0]"/>
-        <param name="score_cutoff" type="float" value="0" label="Score cut-off" min="0" max="2"
+        <param argument="--score_cutoff" type="float" value="0" label="Score cut-off" min="0" max="2"
                help="Hybrids with less than this score will be discarded in the final output. [0-2.0]"/>
-        <param name="chimeric_overlap" type="integer" value="2"
+        <param argument="--chimeric_overlap" type="integer" value="2"
                label=" Maximum number of bases allowed between the chimericsegments of a read"/>
         <conditional name="reference">
             <param name="ref_type" type="select" label="Did you use single or split reference for alignment?">
                 <option value="split">Split reference</option>
                 <option value="single">Single reference</option>
             </param>
             <when value="split">
-                <param format="fasta" name="ref_fasta1" type="data" label="Reference FASTA file"
+                <param format="fasta" argument="--ref_fasta1" type="data" label="Reference FASTA file"
                        help="Reference fasta file"/>
-                <param format="fasta" name="ref_fasta2" type="data" label="Second reference FASTA file"
+                <param format="fasta" argument="--ref_fasta2" type="data" label="Second reference FASTA file"
                        help="Second reference fasta file."/>
             </when>
             <when value="single">
-                <param format="fasta" name="ref_fasta" type="data" label="Reference FASTA file"
+                <param format="fasta" argument="--ref_fasta1" name="ref_fasta" type="data" label="Reference FASTA file"
                        help="Reference fasta file"/>
             </when>
         </conditional>
-        <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false"
+        <param argument="--hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false"
                label="Hybridize chimeric loci?"
                help="Turning this option on increases the run time of the tool significantly."/>
-        <param name="intarna_mode" type="select">
+        <param argument="--intarna_mode" type="select">
             <option value="H">Heuristic</option>
             <option value="M">Exact</option>
             <option value="S">Seed-only</option>
         </param>
-        <param name="seed_interaction" type="boolean" truevalue="" falsevalue="--no_seed" checked="true"
+        <param argument="--no_seed" name="seed_interaction" type="boolean" truevalue="" falsevalue="--no_seed" checked="true"
                label="Enforce seed interaction?"/>
-        <param name="seed_bp" type="integer" value="5" min="2" max="20"
+        <param argument="--seed_bp" type="integer" value="5" min="2" max="20"
                label="Number of inter-molecular base pairs within the seed region"
                help="IntaRNA --seedBP parameter"/>
-        <param name="seed_min_pu" type="float" value="0" min="0" max="1"
+        <param argument="--seed_min_pu" type="float" value="0" min="0" max="1"
                label="Minimal unpaired probability (per sequence) a seed region may have"
                help="IntaRNA --seedMinPu parameter"/>
-        <param name="accessibility" type="boolean" truevalue="C" falsevalue="N" checked="false"
+        <param argument="--accessibility" type="boolean" truevalue="C" falsevalue="N" checked="false"
                label="Compute accessibility profiles for interacting sequences?"/>
-        <param name="acc_width" type="integer" value="150" min="0" max="99999"
+        <param argument="--acc_width" type="integer" value="150" min="0" max="99999"
                label="Sliding window size for accessibility computation"
                help="IntaRNA --accW parameter"/>
-        <param name="temperature" type="float" value="37" min="0" max="100"
+        <param argument="--temperature" type="float" value="37" min="0" max="100"
                label="IntaRNA temperature parameter in Celsius to setup the VRNA energy parameters"/>
-        <param name="summarize" type="boolean" truevalue="-s" falsevalue="" checked="false"
+        <param argument="--summerize" name="summarize" type="boolean" truevalue="-s" falsevalue="" checked="false"
                label="Summarize interactions at loci level?"/>
     </inputs>
 

tools/chira/chira_map.xml

@@ -1,9 +1,9 @@
-<tool id="chira_map" name="ChiRA map" version="@WRAPPER_VERSION@0">
+<tool id="chira_map" name="ChiRA map" version="@TOOL_VERSION@0">
     <description>map reads to trascriptome</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command detect_errors="aggressive"><![CDATA[
         chira_map.py -b
@@ -123,7 +123,6 @@
             <param name="ref_type" value="split"/>
             <param name="ref_fasta1" value="ref1.fasta"/>
             <param name="ref_fasta2" value="ref2.fasta"/>
-            <param name="unmapped" value="True"/>
             <output name="mapped_bed" >
                 <assert_contents>
                     <has_text_matching expression="mmu-miR-6898-5p\t11\t21\t2\|2,mmu-miR-6898-5p,11,21,\+,10M39S\t1\t\+" />
@@ -142,7 +141,6 @@
             <param name="ref_type" value="split"/>
             <param name="ref_fasta1" value="ref1.fasta"/>
             <param name="ref_fasta2" value="ref2.fasta"/>
-            <param name="unmapped" value="True"/>
             <output name="mapped_bed" >
                 <assert_contents>
                     <has_text_matching expression="mmu-miR-20a-5p\t0\t23\t3\|2,mmu-miR-20a-5p,0,23,\+,5S23M27S\t1\t\+" />
@@ -167,7 +165,7 @@ This tool handles the mapping of the reads to reference transcriptome. User can
 **Output**
 
 * BED file containing the alignments
-* Optional unmapped FASTA file
+* unmapped FASTA file (only for aligner BWA-MEM)
 
     </help>
     <expand macro="citations" />

tools/chira/chira_merge.xml

@@ -1,9 +1,9 @@
-<tool id="chira_merge" name="ChiRA merge" version="@WRAPPER_VERSION@0">
+<tool id="chira_merge" name="ChiRA merge" version="@TOOL_VERSION@0">
     <description>merge aligned positions</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command><![CDATA[
         chira_merge.py

tools/chira/chira_quantify.xml

@@ -1,9 +1,9 @@
-<tool id="chira_quantify" name="ChiRA qauntify" version="@WRAPPER_VERSION@0">
+<tool id="chira_quantify" name="ChiRA qauntify" version="@TOOL_VERSION@0">
     <description>quantify aligned loci to score the alignments</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command><![CDATA[
         chira_quantify.py

tools/chira/macros.xml

@@ -1,5 +1,5 @@
 <macros>
-    <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy</token>
+    <token name="@TOOL_VERSION@">@TOOL_VERSION@+galaxy</token>
     <token name="@TOOL_VERSION@">1.4.3</token>
     <xml name="bio_tools">
         <xrefs>