Merge pull request #2210 from pvanheus/maskFastaBedtoolsFix

bedtools maskfasta: fullheader to fullHeader
galaxyproject · Dec 17, 2018 · 0a8cabc · 0a8cabc
2 parents 2833624 + 76c057a
commit 0a8cabc
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Showing 5 changed files with 17 additions and 4 deletions.
diff --git a/tools/bedtools/maskFastaBed.xml b/tools/bedtools/maskFastaBed.xml
@@ -25,7 +25,7 @@
         <param name="mc" type="text"  value="N"
             label="Replace masking character"
             help="That is, instead of masking with Ns, use another character. (-mc)" />
-        <param argument="-fullheader" type="boolean" truevalue="-fullheader" falsevalue=""
+        <param argument="-fullHeader" name="fullheader" type="boolean" truevalue="-fullHeader" falsevalue=""
             label="Use full fasta header." 
             help="By default, only the word before the first space or tab is used"/>
     </inputs>
@@ -37,13 +37,20 @@
             <param name="input" value="nucBed1.bed" ftype="bed" />
             <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
             <param name="soft" value="False" />
-            <output name="output" file="maskFastaBed_result1.bed" ftype="fasta" />
+            <output name="output" file="maskFastaBed_result1.fasta" ftype="fasta" />
         </test>
         <test>
             <param name="input" value="nucBed1.bed" ftype="bed" />
             <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
             <param name="soft" value="True" />
-            <output name="output" file="maskFastaBed_result2.bed" ftype="fasta" />
+            <output name="output" file="maskFastaBed_result2.fasta" ftype="fasta" />
+        </test>
+        <test>
+            <param name="input" value="nucBed1.bed" ftype="bed" />
+            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
+            <param name="soft" value="True" />
+            <param name="fullheader" value="True" />
+            <output name="output" file="maskFastaBed_result3.fasta" ftype="fasta" />
         </test>
     </tests>
     <help>

diff --git a/...dtools/test-data/maskFastaBed_result1.bed → ...ools/test-data/maskFastaBed_result1.fasta b/...dtools/test-data/maskFastaBed_result1.bed → ...ools/test-data/maskFastaBed_result1.fasta
diff --git a/...dtools/test-data/maskFastaBed_result2.bed → ...ools/test-data/maskFastaBed_result2.fasta b/...dtools/test-data/maskFastaBed_result2.bed → ...ools/test-data/maskFastaBed_result2.fasta
diff --git a/tools/bedtools/test-data/maskFastaBed_result3.fasta b/tools/bedtools/test-data/maskFastaBed_result3.fasta
@@ -0,0 +1,6 @@
+>chr1 description
+GACTCATGATttcttacctattagtggttgaacatcgtgatatgtatgttgacggccataaggctgcttcttgttgtcga
+tagaacttcatgtgcctgtaAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA
+TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG
+TGGACTGCTGGCGTTATAACGCCGAAGCGGTAAAAATTTTTATTTTTTTTCTCACTTCTGTTACTCCAGCTTCTTCGGCA
+CCTGTGGCCTGTTGATTCTAAAGGTTAGTTTCTTCACGC
diff --git a/tools/bedtools/test-data/nucBed1.fasta b/tools/bedtools/test-data/nucBed1.fasta
@@ -1,4 +1,4 @@
->chr1
+>chr1 description
 GACTCATGATTTCTTACCTATTAGTGGTTGAACATCGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTTGTTGTCGA
 TAGAACTTCATGTGCCTGTAAAACAAGTACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTAGCGTTTATGTTGGTTTCA
 TGGTTTTGTCTAACTTTATCGCTTTACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCTTGTTTACGAATTAAATCGAAG