Mercurial > repos > jpayne > gtsubsampler

comparison reads_subsampler.xml @ 5:3852b3edc8a4 tip

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"planemo upload for repository https://toolrepo.galaxytrakr.org/"
author jpayne
date Fri, 19 Feb 2021 17:51:59 -0500
parents 504004e78363
children
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4:a90a883f88f9 5:3852b3edc8a4
4 <requirement type="package" version="3.7">python</requirement> 4 <requirement type="package" version="3.7">python</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 #if $reads.reads_select == 'collection' 7 #if $reads.reads_select == 'collection'
8 python3 ${__tool_directory__}/subsamplr.py '$reads.coll.forward' '$reads.coll.reverse' '$downsampled.forward' '$downsampled.reverse' $coverage $genome_size '$seed' 8 python3 ${__tool_directory__}/subsamplr.py '$reads.coll.forward' '$reads.coll.reverse' '$downsampled.forward' '$downsampled.reverse' $coverage $genome_size '$seed'
9 #else 9 #elif $reads.reads_select == 'single'
10 #if $reverse 10 python3 ${__tool_directory__}/subsamplr.py '$forward' '$forward_out' $coverage $genome_size '$seed'
11 python3 ${__tool_directory__}/subsamplr.py '$forward' '$reverse' $forward_out $reverse_out $coverage $genome_size '$seed' 11 #else
12 #else 12 python3 ${__tool_directory__}/subsamplr.py '$forward' '$reverse' $forward_out $reverse_out $coverage $genome_size '$seed'
13 python3 ${__tool_directory__}/subsamplr.py '$forward' '$forward_out' $coverage $genome_size '$seed'
14 #end if
15 #end if 13 #end if
16 ]]></command> 14 ]]></command>
17 <inputs> 15 <inputs>
18 <conditional name="reads"> 16 <conditional name="reads">
19 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history"> 17 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
32 <param label="Reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" /> 30 <param label="Reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
33 </when> 31 </when>
34 </conditional> 32 </conditional>
35 <param name="coverage" type="integer" label="Maximum Coverage" value="200" /> 33 <param name="coverage" type="integer" label="Maximum Coverage" value="200" />
36 <param name="genome_size" type="select" label="Assumed Genome Size"> 34 <param name="genome_size" type="select" label="Assumed Genome Size">
37 <option value="4500000">Salmonella, E. Coli (4500000)</option> 35 <option value="5000000">Salmonella, E. Coli, Vibrio p. (5000000)</option>
36 <option value="4000000">Vibrio cholerae (4000000)</option>
38 <option value="2700000">Listeria (2700000)</option> 37 <option value="2700000">Listeria (2700000)</option>
38 <option value="1600000">Campylobacter (1600000)</option>
39 <option value="29900">SARS-CoV-2 (29900)</option> 39 <option value="29900">SARS-CoV-2 (29900)</option>
40 </param> 40 </param>
41 <param name="seed" type="text" value="ed2b99d842cddc1ac81d7c01a0bf0555" label="Random seed (you don't have to change this)"/> 41 <param name="seed" type="text" value="ed2b99d842cddc1ac81d7c01a0bf0555" label="Random seed (you don't have to change this)"/>
42 </inputs> 42 </inputs>
43 <outputs> 43 <outputs>
52 <data name="forward" label="${reads.coll.forward.name}.downsampled" format_source="reads.coll.forward" /> 52 <data name="forward" label="${reads.coll.forward.name}.downsampled" format_source="reads.coll.forward" />
53 <data name="reverse" label="${reads.coll.reverse.name}.downsampled" format_source="reads.coll.reverse" /> 53 <data name="reverse" label="${reads.coll.reverse.name}.downsampled" format_source="reads.coll.reverse" />
54 </collection> 54 </collection>
55 </outputs> 55 </outputs>
56 <tests> 56 <tests>
57 <test>
58 <conditional name="reads">
59 <param name="reads_select" value="single" />
60 <param name="forward" value="forward.fastq" />
61 </conditional>
62 <param name="coverage" value="20" />
63 <param name="genome_size" value="29900" />
64 <output name="forward_out" value="forward_out.fastq" />
65 </test>
57 <test> 66 <test>
58 <conditional name="reads"> 67 <conditional name="reads">
59 <param name="reads_select" value="collection" /> 68 <param name="reads_select" value="collection" />
60 <param name="coll"> 69 <param name="coll">
61 <collection type="paired"> 70 <collection type="paired">