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comparison interval2maf.xml @ 2:1080e07a2233 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit 9f522562ca2048b8bafa3404abf3f930f72f7f05
author iuc
date Wed, 09 Nov 2022 12:34:55 +0000
parents b79f6002b176
children
comparison
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1:b79f6002b176 2:1080e07a2233
1 <tool id="Interval2Maf1" name="Extract MAF blocks" version="1.0.1+galaxy0"> 1 <tool id="Interval2Maf1" name="Extract MAF blocks" version="1.0.1+galaxy1" profile="21.05">
2 <description>given a set of genomic intervals</description> 2 <description>given a set of genomic intervals</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <xrefs>
7 <expand macro="requirements" /> 7 <xref type="bio.tools">bx-python</xref>
8 </requirements> 8 </xrefs>
9 <expand macro="requirements" />
9 <command> 10 <command>
10 <![CDATA[ 11 <![CDATA[
11 #if $maf_source_type.maf_source == "cached" 12 #if $maf_source_type.maf_source == "cached"
12 #set $tab = '\t' 13 #set $tab = '\t'
13 echo "$maf_source_type.mafType.fields.name${tab}$maf_source_type.mafType.fields.value${tab}$maf_source_type.mafType.fields.indexed_for${tab}$maf_source_type.mafType.fields.exists_in_maf${tab}$maf_source_type.mafType.fields.path" >> ./maf_indexes.loc && 14 echo "$maf_source_type.mafType.fields.name${tab}$maf_source_type.mafType.fields.value${tab}$maf_source_type.mafType.fields.indexed_for${tab}$maf_source_type.mafType.fields.exists_in_maf${tab}$maf_source_type.mafType.fields.path" >> ./maf_indexes.loc &&
77 <outputs> 78 <outputs>
78 <data format="maf" name="out_file1"/> 79 <data format="maf" name="out_file1"/>
79 </outputs> 80 </outputs>
80 <tests> 81 <tests>
81 <test> 82 <test>
82 <param name="input1" dbkey="hg38" value="interval2maf-in1.bed" /> 83 <param name="input1" dbkey="hg38" value="interval2maf-in.bed" />
83 <param name="maf_source" value="user" /> 84 <param name="maf_source" value="user" />
84 <param name="mafFile" dbkey="hg38" value="interval2maf-in1.maf" /> 85 <param name="mafFile" dbkey="hg38" value="interval2maf-in1.maf" />
85 <param name="species" value="hg38,mm10,eulFla1" /> 86 <param name="species" value="hg38,mm10,eulFla1" />
86 <param name="split_blocks_by_species" value="dont_split_blocks_by_species"/> 87 <param name="split_blocks_by_species" value="dont_split_blocks_by_species"/>
87 <output name="out_file1" file="interval2maf-out1.maf" /> 88 <output name="out_file1" file="interval2maf-out1.maf" />
88 </test> 89 </test>
89 <test> 90 <test>
90 <param name="input1" dbkey="hg38" value="interval2maf-in2.bed"/> 91 <param name="input1" dbkey="hg38" value="interval2maf-in.bed"/>
91 <param name="maf_source" value="cached"/> 92 <param name="maf_source" value="cached"/>
92 <param name="mafType" value="TEST"/> 93 <param name="mafType" value="TEST"/>
93 <param name="species" value="hg38,mm10,eulFla1" /> 94 <param name="species" value="hg38,mm10,eulFla1" />
94 <param name="split_blocks_by_species" value="dont_split_blocks_by_species"/> 95 <param name="split_blocks_by_species" value="dont_split_blocks_by_species"/>
95 <output name="out_file1" file="interval2maf-out2.maf" /> 96 <output name="out_file1" file="interval2maf-out2.maf" />
96 </test> 97 </test>
97 <test> 98 <test>
98 <param name="input1" dbkey="hg38" value="interval2maf-in3.bed"/> 99 <param name="input1" dbkey="hg38" value="interval2maf-in.bed"/>
99 <param name="maf_source" value="cached"/> 100 <param name="maf_source" value="cached"/>
100 <param name="mafType" value="TEST"/> 101 <param name="mafType" value="TEST"/>
101 <param name="species" value="hg38,mm10,eulFla1" /> 102 <param name="species" value="hg38,mm10,eulFla1" />
102 <param name="split_blocks_by_species" value="dont_split_blocks_by_species"/> 103 <param name="split_blocks_by_species" value="dont_split_blocks_by_species"/>
103 <output name="out_file1" file="interval2maf-out3.maf" /> 104 <output name="out_file1" file="interval2maf-out3.maf" />