Mercurial > repos > iuc > stacks_ustacks

comparison stacks_ustacks.xml @ 4:ff04b3748654 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
author iuc
date Mon, 26 Sep 2016 11:45:47 -0400
parents 216c469422d2
children dc96f579ef90
comparison
equal deleted inserted replaced
3:216c469422d2 4:ff04b3748654
1 <tool id="stacks_ustacks" name="Stacks: ustacks" version="@WRAPPER_VERSION@.1"> 1 <tool id="stacks_ustacks" name="Stacks: ustacks" version="@WRAPPER_VERSION@.0">
2 <description>align short reads into stacks</description> 2 <description>align short reads into stacks</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
36 -f $data_path 36 -f $data_path
37 37
38 -t $inputype 38 -t $inputype
39 39
40 ## Batch description 40 ## Batch description
41 -i $sample_id 41 -i 1
42 42
43 -m $m 43 -m $m
44 -M $M 44 -M $M
45 $R 45 $R
46 $H 46 $H
79 ]]></command> 79 ]]></command>
80 80
81 <inputs> 81 <inputs>
82 <param name="sample" argument="-f" format="fastqsanger,fasta" type="data" label="Input short reads from an individual" /> 82 <param name="sample" argument="-f" format="fastqsanger,fasta" type="data" label="Input short reads from an individual" />
83 83
84 <param name="sample_id" argument="-i" type="integer" value="" label="Give a unique numeric ID to this sample"/>
85
86 <param name="m" argument="-m" type="integer" value="2" label="Minimum depth of coverage required to create a stack"/> 84 <param name="m" argument="-m" type="integer" value="2" label="Minimum depth of coverage required to create a stack"/>
87 <param name="M" argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/> 85 <param name="M" argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/>
88 <param name="R" argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads" /> 86 <param name="R" argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads" />
89 <param name="H" argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" /> 87 <param name="H" argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" />
90 88
113 <outputs> 111 <outputs>
114 <data format="txt" name="output_log" label="ustacks.log with ${tool.name} on ${on_string}" from_work_dir="ustacks.log" /> 112 <data format="txt" name="output_log" label="ustacks.log with ${tool.name} on ${on_string}" from_work_dir="ustacks.log" />
115 113
116 <collection name="tabs" type="list" label="Stacks from ${on_string}"> 114 <collection name="tabs" type="list" label="Stacks from ${on_string}">
117 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" /> 115 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
118 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />> 116 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
119 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" /> 117 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
120 <discover_datasets pattern="(?P&lt;name&gt;.+\.models)\.tsv$" ext="tabular" directory="stacks_outputs" /> 118 <discover_datasets pattern="(?P&lt;name&gt;.+\.models)\.tsv$" ext="tabular" directory="stacks_outputs" />
121 </collection> 119 </collection>
122 </outputs> 120 </outputs>
123 121
124 <tests> 122 <tests>
125 <test> 123 <test>
126 <param name="sample" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" /> 124 <param name="sample" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
127 <param name="sample_id" value="4" />
128 125
129 <output name="output_log"> 126 <output name="output_log">
130 <assert_contents> 127 <assert_contents>
131 <has_text text="done." /> 128 <has_text text="done." />
132 </assert_contents> 129 </assert_contents>
194 @STACKS_INFOS@ 191 @STACKS_INFOS@
195 ]]> 192 ]]>
196 </help> 193 </help>
197 <expand macro="citation" /> 194 <expand macro="citation" />
198 </tool> 195 </tool>
199