Mercurial > repos > bgruening > find_subsequences
diff find_subsequences.xml @ 1:d882a0a75759 draft default tip
Uploaded
author | bgruening |
---|---|
date | Fri, 10 Apr 2015 06:49:30 -0400 |
parents | 7f39014f9404 |
children |
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--- a/find_subsequences.xml Fri Mar 20 06:23:17 2015 -0400 +++ b/find_subsequences.xml Fri Apr 10 06:49:30 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="bg_find_subsequences" name="Nucleotide subsequence search" version="0.1"> +<tool id="bg_find_subsequences" name="Nucleotide subsequence search" version="0.2"> <description>providing regions in BED format</description> <requirements> <requirement type="package" version="1.65">biopython</requirement> @@ -6,14 +6,15 @@ <command interpreter="python"> <![CDATA[ find_subsequences.py - --input $input - --output $output + --input "${input}" + --output "${output}" --pattern "$pattern_conditional.pattern" #if $input.ext == 'fasta': --format 'fasta' #else: --format 'fastq' #end if + --strand '$strand' ]]> </command> <inputs> @@ -248,6 +249,11 @@ </param> </when> </conditional> + <param name="strand" type="select" label="Search pattern on"> + <option value='both'>both strands</option> + <option value='forward'>forward strand</option> + <option value='reverse'>reverse strand</option> + </param> </inputs> <outputs> <data format="bed" name="output" /> @@ -271,6 +277,20 @@ <param name="pattern_conditional_select" value="user"/> <output name="output" file="find_subsequences_advanced_result1.bed" ftype="bed"/> </test> + <test> + <param name="input" value="find_subsequences_input1.fasta" ftype="fasta"/> + <param name="pattern" value="atnncg"/> + <param name="strand" value="reverse"/> + <param name="pattern_conditional_select" value="user"/> + <output name="output" file="find_subsequences_advanced_result2.bed" ftype="bed"/> + </test> + <test> + <param name="input" value="find_subsequences_input1.fasta" ftype="fasta"/> + <param name="pattern" value="atnncg"/> + <param name="strand" value="forward"/> + <param name="pattern_conditional_select" value="user"/> + <output name="output" file="find_subsequences_advanced_result3.bed" ftype="bed"/> + </test> </tests> <help> <![CDATA[