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comparison seqPrep.xml @ 1:d1130c342dc9 draft

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"planemo upload for repository https://github.com/galaxy-works/shed-tools/tree/main/tools/seqprep commit f933f2d9276c45dbcd5e34a4e6c27c1f0029d016"
author galaxyworks
date Sun, 28 Feb 2021 21:52:26 +0000
parents f25733322c54
children dd2c54f4a12e
comparison
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0:f25733322c54 1:d1130c342dc9
1 <tool id="seqprep" name="SeqPrep" version="0.2.0"> 1 <tool id="seqprep" name="SeqPrep" version="0.2.1">
2 <description>merge paired end Illumina reads</description> 2 <description>merge paired end Illumina reads</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.3.2">seqprep</requirement> 4 <requirement type="package" version="1.3.2">seqprep</requirement>
5 <requirement type="package" version="3.7">python</requirement> 5 <requirement type="package" version="3.7">python</requirement>
6 </requirements> 6 </requirements>
89 #end if 89 #end if
90 #if $merge.n 90 #if $merge.n
91 -n $merge.n 91 -n $merge.n
92 #end if 92 #end if
93 -s merge.gz 93 -s merge.gz
94 && zcat -f merge.gz > '$s'
94 #if $merge.lengths_select 95 #if $merge.lengths_select
95 && zcat -f merge.gz > '$s' 96 && cat '$s' | python '$__tool_directory__/seqlens.py' > '$s_lengths'
96 && cat '$s' | python '$__tool_directory__/seqlens.py' > '$s_lengths' 97 #end if
97 #end if 98 #end if
98 && zcat -f one.gz > '$one' 99 && zcat -f one.gz > '$one'
99 && zcat -f two.gz > '$two' 100 && zcat -f two.gz > '$two'
100 #if $save_discarded 101 #if $save_discarded
101 && zcat -f three.gz > '$three' 102 && zcat -f three.gz > '$three'
102 && zcat -f found.gz > '$four' 103 && zcat -f found.gz > '$four'
103 #end if
104 #end if 104 #end if
105 ]]></command> 105 ]]></command>
106 <inputs> 106 <inputs>
107 <param name="f" type="data" format="fastq,fastqillumina,fastqsanger,fastqsolexa" label="Forward reads" /> 107 <param name="f" type="data" format="fastq,fastqillumina,fastqsanger,fastqsolexa" label="Forward reads" />
108 <param name="r" type="data" format="fastq,fastqillumina,fastqsanger,fastqsolexa" label="Reverse reads" /> 108 <param name="r" type="data" format="fastq,fastqillumina,fastqsanger,fastqsolexa" label="Reverse reads" />