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comparison presto_pairseq.xml @ 4:eed465eb14a3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 1beb51cefbe9e6edc8930c7ae0421f28e7bb93c8
author iuc
date Fri, 04 Oct 2024 09:04:27 +0000
parents 49e7407445c3
children
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3:49e7407445c3 4:eed465eb14a3
1 <tool id="presto_pairseq" name="pRESTO PairSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="presto_pairseq" name="pRESTO PairSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Sorts and matches sequence records with matching coordinates across files</description> 2 <description>Sorts and matches sequence records with matching coordinates across files</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>presto_macros.xml</import> 4 <import>presto_macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 7
8 <expand macro="requirements"/> 8 <expand macro="requirements"/>
9 9
10 <version_command>PairSeq.py --version</version_command> 10 <version_command>PairSeq.py --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
36 </param> 36 </param>
37 <expand macro="presto-coord-param"/> 37 <expand macro="presto-coord-param"/>
38 <param argument="--failed" type="boolean" checked="false" truevalue="--failed" falsevalue="" label="Failed reads fastq output" /> 38 <param argument="--failed" type="boolean" checked="false" truevalue="--failed" falsevalue="" label="Failed reads fastq output" />
39 </inputs> 39 </inputs>
40 <outputs> 40 <outputs>
41 <data name="r1_out" format="fastq" from_work_dir="tmp-1_pair-pass.fastq"/> 41 <data name="r1_out" format="fastq" from_work_dir="tmp-1_pair-pass.fastq" label="${tool.name} on ${on_string}: Paired R1"/>
42 <data name="r2_out" format="fastq" from_work_dir="tmp-2_pair-pass.fastq"/> 42 <data name="r2_out" format="fastq" from_work_dir="tmp-2_pair-pass.fastq" label="${tool.name} on ${on_string}: Paired R2"/>
43 <!-- only give these 2 outputs if input failed_fastq=True--> 43 <!-- only give these 2 outputs if input failed_fastq=True-->
44 <data name="r1_fail_out" format="fastq" from_work_dir="tmp-1_pair-fail.fastq"> 44 <data name="r1_fail_out" format="fastq" from_work_dir="tmp-1_pair-fail.fastq" label="${tool.name} on ${on_string}: Unpaired R1">
45 <filter>failed</filter> 45 <filter>failed</filter>
46 </data> 46 </data>
47 <data name="r2_fail_out" format="fastq" from_work_dir="tmp-2_pair-fail.fastq"> 47 <data name="r2_fail_out" format="fastq" from_work_dir="tmp-2_pair-fail.fastq" label="${tool.name} on ${on_string}: Unpaired R2">
48 <filter>failed</filter> 48 <filter>failed</filter>
49 </data> 49 </data>
50 </outputs> 50 </outputs>
51 <tests> 51 <tests>
52 <test expect_num_outputs="2"> 52 <test expect_num_outputs="2">