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comparison bwameth.xml @ 7:c4549c37e18e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 6d44811a45b4f6fded1ec72450ed300318095ce4"
author iuc
date Tue, 13 Jul 2021 13:56:02 +0000
parents 368c79aa228f
children 986033b71bbc
comparison
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6:368c79aa228f 7:c4549c37e18e
1 <tool id="bwameth" name="bwameth" version="@TOOL_VERSION@" profile="17.01"> 1 <tool id="bwameth" name="bwameth" version="@TOOL_VERSION@+galaxy1" profile="20.05">
2 <description>Fast and accurate aligner of BS-Seq reads.</description> 2 <description>Fast and accurate aligner of BS-Seq reads.</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">0.2.2</token> 4 <token name="@TOOL_VERSION@">0.2.2</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
76 #if $single_or_paired.single_or_paired_opts == 'single': 76 #if $single_or_paired.single_or_paired_opts == 'single':
77 $read1 77 $read1
78 #else: 78 #else:
79 $read1 $read2 79 $read1 $read2
80 #end if 80 #end if
81 | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" -O bam -o output.bam - 81 | samtools view --no-PG -u - | samtools sort --no-PG -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" -O bam -o output.bam -
82 ]]></command> 82 ]]></command>
83 <inputs> 83 <inputs>
84 <conditional name="referenceSource"> 84 <conditional name="referenceSource">
85 <param name="source" type="select" label="Select a genome reference from your history or a built-in index?"> 85 <param name="source" type="select" label="Select a genome reference from your history or a built-in index?">
86 <option value="history" selected="True">Use one from the history</option> 86 <option value="history" selected="True">Use one from the history</option>
128 <param name="referenceSource" value="history" /> 128 <param name="referenceSource" value="history" />
129 <param name="reference" value="ref.fa.gz" /> 129 <param name="reference" value="ref.fa.gz" />
130 <param name="single_or_paired_opts" value="paired" /> 130 <param name="single_or_paired_opts" value="paired" />
131 <param name="input_mate1" value="t_R1.fastq.gz"/> 131 <param name="input_mate1" value="t_R1.fastq.gz"/>
132 <param name="input_mate2" value="t_R2.fastq.gz"/> 132 <param name="input_mate2" value="t_R2.fastq.gz"/>
133 <output file="output.bam" ftype="bam" name="output" lines_diff="2"/> 133 <output file="output.bam" ftype="bam" name="output" lines_diff="4"/><!-- allow for HD and PG lines diff-->
134 </test> 134 </test>
135 <test> 135 <test>
136 <param name="referenceSource" value="history" /> 136 <param name="referenceSource" value="history" />
137 <param name="reference" value="ref.fa.gz" /> 137 <param name="reference" value="ref.fa.gz" />
138 <param name="single_or_paired_opts" value="paired_collection" /> 138 <param name="single_or_paired_opts" value="paired_collection" />
140 <collection type="paired"> 140 <collection type="paired">
141 <element name="forward" value="t_R1.fastq.gz"/> 141 <element name="forward" value="t_R1.fastq.gz"/>
142 <element name="reverse" value="t_R2.fastq.gz"/> 142 <element name="reverse" value="t_R2.fastq.gz"/>
143 </collection> 143 </collection>
144 </param> 144 </param>
145 <output file="output.bam" ftype="bam" name="output" lines_diff="2"/> 145 <output file="output.bam" ftype="bam" name="output" lines_diff="4"/><!-- allow for HD and PG lines diff-->
146 </test> 146 </test>
147 </tests> 147 </tests>
148 <help><![CDATA[ 148 <help><![CDATA[
149 149
150 **What it does** 150 **What it does**