Mercurial > repos > jackcurragh > ribogalaxy_get_chrom_sizes

diff get_chrom_sizes/get_chrom_sizes.xml @ 3:cfdf764b9226 draft

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author jackcurragh
date Thu, 21 Apr 2022 10:39:18 +0000
parents 27f3669eda60
children c6a297d05c8e
line wrap: on
line diff
--- a/get_chrom_sizes/get_chrom_sizes.xml	Wed Apr 20 15:20:33 2022 +0000
+++ b/get_chrom_sizes/get_chrom_sizes.xml	Thu Apr 21 10:39:18 2022 +0000
@@ -1,10 +1,12 @@
 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.0">
     <description>Chromosome sizes are needed for the creation of ribosome profiles. This tool generates a tab delimited chrom.sizes file from an inputted fasta</description>
     <command>
-        python $__tool_directory__/calculating_chrom.sizes.py ${input1} ${output1}
+        python $__tool_directory__/calculating_chrom.sizes.py ${input1} ${input2} ${output1}
     </command>
     <inputs>
         <param name="input1" type="data" format="fasta" label="FASTA File" />
+        <param name="input2" type="text" label="Chromosome Column Prefix (eg. chr)" />
+
     </inputs>
     <outputs>
        <data name="output1" format="tabular"/>
@@ -12,6 +14,7 @@
     <tests>
         <test>
             <param name="input1" value="test.fasta" ftype="fasta" />
+            <param name="input2" value="chr"/>
             <output name="output1" file="test.fasta.sizes" ftype="tabular" lines_diff="4" />
         </test>
     </tests>