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comparison samblaster.xml @ 2:c07ffa5e508d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 2bcb9bf1c90bee25a100f14f8ea28909aba89c9a
author iuc
date Sat, 05 Oct 2024 13:29:29 +0000
parents de6d84a9bc8f
children 595c942ad3ad
comparison
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1:de6d84a9bc8f 2:c07ffa5e508d
1 <tool id="samblaster" name="samblaster" version="0.1.24"> 1 <tool id="samblaster" name="samblaster" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1">
2 <description>marks duplicates, outputs split reads, discordant read pairs and unmapped reads</description> 2 <description>marks duplicates, outputs split reads, discordant read pairs and unmapped reads</description>
3 <macros>
4 <token name="@TOOL_VERSION@">0.1.24</token>
5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros>
3 <xrefs> 7 <xrefs>
4 <xref type="bio.tools">samblaster</xref> 8 <xref type="bio.tools">samblaster</xref>
5 </xrefs> 9 </xrefs>
6 <requirements> 10 <requirements>
7 <requirement type="package" version="0.1.24">samblaster</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">samblaster</requirement>
8 <requirement type="package" version="0.6.5">sambamba</requirement> 12 <requirement type="package" version="0.6.5">sambamba</requirement>
9 </requirements> 13 </requirements>
10 <version_command>samblaster --version</version_command> 14 <version_command>samblaster --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[ 15 <command detect_errors="exit_code"><![CDATA[
12 #if $input.is_of_type('sam'): 16 #if $input.is_of_type('sam'):
56 <param argument="--minIndelSize" label="Minimum structural variant feature size for split alignments to be included in splitter file." type="integer" value="50" min="1"/> 60 <param argument="--minIndelSize" label="Minimum structural variant feature size for split alignments to be included in splitter file." type="integer" value="50" min="1"/>
57 <param argument="--minNonOverlap" label="Minimum non-overlaping base pairs between two alignments for a read to be included in splitter file." type="integer" value="20" min="1"/> 61 <param argument="--minNonOverlap" label="Minimum non-overlaping base pairs between two alignments for a read to be included in splitter file." type="integer" value="20" min="1"/>
58 <param argument="--minClipSize" label="Minumum number of bases a mapped read must be clipped to be included in unmapped file." type="integer" value="20" min="1"/> 62 <param argument="--minClipSize" label="Minumum number of bases a mapped read must be clipped to be included in unmapped file." type="integer" value="20" min="1"/>
59 </inputs> 63 </inputs>
60 <outputs> 64 <outputs>
61 <data name="output_bam" format="bam" label="samblaster alignments on ${on_string}" from_work_dir="output.bam"> 65 <data name="output_bam" format="bam" label="${tool.name} on ${on_string}: alignments" from_work_dir="output.bam">
62 <filter>output</filter> 66 <filter>output</filter>
63 </data> 67 </data>
64 <data name="discordant_bam" format="bam" label="samblaster discordant alignments on ${on_string}" from_work_dir="discordant.bam"> 68 <data name="discordant_bam" format="bam" label="${tool.name} on ${on_string}discordant alignments" from_work_dir="discordant.bam">
65 <filter>discordantFile</filter> 69 <filter>discordantFile</filter>
66 </data> 70 </data>
67 <data name="splitter_bam" format="bam" label="samblaster split alignments on ${on_string}" from_work_dir="splitter.bam"> 71 <data name="splitter_bam" format="bam" label="${tool.name} on ${on_string}: split alignments" from_work_dir="splitter.bam">
68 <filter>splitterFile</filter> 72 <filter>splitterFile</filter>
69 </data> 73 </data>
70 <data name="unmapped_fastq" format="fastqsanger" label="samblaster unmapped fastq on ${on_string}" from_work_dir="unmapped.fastq"> 74 <data name="unmapped_fastq" format="fastqsanger" label="${tool.name} on ${on_string}: unmapped fastq" from_work_dir="unmapped.fastq">
71 <filter>unmappedFile</filter> 75 <filter>unmappedFile</filter>
72 </data> 76 </data>
73 </outputs> 77 </outputs>
74 <tests> 78 <tests>
75 <test> 79 <test expect_num_outputs="3">
76 <param name="input" value="sr.input.bam"/> 80 <param name="input" value="sr.input.bam"/>
77 <param name="output" value="true"/> 81 <param name="output" value="true"/>
78 <param name="discordandFile" value="false"/> 82 <param name="discordantFile" value="false"/>
79 <param name="splitterFile" value="true"/> 83 <param name="splitterFile" value="true"/>
80 <param name="unmappedFile" value="true"/> 84 <param name="unmappedFile" value="true"/>
81 <output name="output_bam" file="output.bam" compare="sim_size"/> 85 <output name="output_bam" file="output.bam" compare="sim_size"/>
82 <output name="splitter_bam" file="splitters.bam" compare="sim_size"/> 86 <output name="splitter_bam" file="splitters.bam" compare="sim_size"/>
83 <output name="unmapped_fastq"> 87 <output name="unmapped_fastq">
84 <assert_contents> 88 <assert_contents>
85 <has_line line="@M00860:26:000000000-A6UGV:1:1101:10000:6072" /> 89 <has_line line="@M00860:26:000000000-A6UGV:1:1101:10000:6072" />
86 </assert_contents> 90 </assert_contents>
87 </output> 91 </output>
88 </test> 92 </test>
89 <test> 93 <test expect_num_outputs="3">
90 <param name="input" value="sr.input.sam.gz" ftype="sam"/> 94 <param name="input" value="sr.input.sam.gz" ftype="sam"/>
91 <param name="output" value="true"/> 95 <param name="output" value="true"/>
92 <param name="discordandFile" value="false"/> 96 <param name="discordantFile" value="false"/>
93 <param name="splitterFile" value="true"/> 97 <param name="splitterFile" value="true"/>
94 <param name="unmappedFile" value="true"/> 98 <param name="unmappedFile" value="true"/>
95 <output name="output_bam" file="output.bam" compare="sim_size"/> 99 <output name="output_bam" file="output.bam" compare="sim_size"/>
96 <output name="splitter_bam" file="splitters.bam" compare="sim_size"/> 100 <output name="splitter_bam" file="splitters.bam" compare="sim_size"/>
97 <output name="unmapped_fastq"> 101 <output name="unmapped_fastq">