Mercurial > repos > iuc > stacks_rxstacks

comparison stacks_rxstacks.xml @ 3:55814b6afe69 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
author iuc
date Sat, 25 Jun 2016 17:27:52 -0400
parents a1f5a4be394a
children fec69a2d92d7
comparison
equal deleted inserted replaced
2:77f5db795774 3:55814b6afe69
1 <tool id="stacks_rxstacks" name="Stacks: rxstacks" version="@WRAPPER_VERSION@.0"> 1 <tool id="stacks_rxstacks" name="Stacks: rxstacks" version="@WRAPPER_VERSION@.1">
2 <description>make corrections to genotype and haplotype calls</description> 2 <description>make corrections to genotype and haplotype calls</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"/>
11 11
12 && 12 &&
13 13
14 #for $input_file in $input_col: 14 #for $input_file in $input_col:
15 #set $ext = "" 15 #set $ext = ""
16 #if not str($input_file.name).endswith('.tsv'): 16 #if not str($input_file.element_identifier).endswith('.tsv'):
17 #set $ext = ".tsv" 17 #set $ext = ".tsv"
18 #end if 18 #end if
19 ln -s "${input_file}" "stacks_inputs/${input_file.name}${ext}" && 19 ln -s "${input_file}" "stacks_inputs/${input_file.element_identifier}${ext}" &&
20 #end for 20 #end for
21 21
22 rxstacks 22 rxstacks
23 23
24 -t \${GALAXY_SLOTS:-1} 24 -t \${GALAXY_SLOTS:-1}
93 <data format="txt" name="output_lnl_dist" label="Distribution of mean log likelihoods with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.rxstacks_lnls.tsv"> 93 <data format="txt" name="output_lnl_dist" label="Distribution of mean log likelihoods with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.rxstacks_lnls.tsv">
94 <filter>options_filtering['lnl_dist']</filter> 94 <filter>options_filtering['lnl_dist']</filter>
95 </data> 95 </data>
96 96
97 <collection name="tags" type="list" label="Assembled loci filtered from ${on_string}"> 97 <collection name="tags" type="list" label="Assembled loci filtered from ${on_string}">
98 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv" ext="tabular" directory="stacks_outputs" /> 98 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
99 </collection> 99 </collection>
100 100
101 <collection name="snps" type="list" label="Model calls from each locus filtered from ${on_string}"> 101 <collection name="snps" type="list" label="Model calls from each locus filtered from ${on_string}">
102 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv" ext="tabular" directory="stacks_outputs" /> 102 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
103 </collection> 103 </collection>
104 104
105 <collection name="alleles" type="list" label="Haplotypes/alleles recorded from each locus filtered from ${on_string}"> 105 <collection name="alleles" type="list" label="Haplotypes/alleles recorded from each locus filtered from ${on_string}">
106 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv" ext="tabular" directory="stacks_outputs" /> 106 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
107 </collection> 107 </collection>
108 108
109 <collection name="all_output" type="list" label="Full output from rxstacks on ${on_string}"> 109 <collection name="all_output" type="list" label="Full output from rxstacks on ${on_string}">
110 <discover_datasets pattern="(?P&lt;name&gt;.+\.(tags|snps|alleles))\.tsv" ext="tabular" directory="stacks_outputs" /> 110 <discover_datasets pattern="(?P&lt;name&gt;.+\.(tags|snps|alleles))\.tsv$" ext="tabular" directory="stacks_outputs" />
111 </collection> 111 </collection>
112 </outputs> 112 </outputs>
113 113
114 <tests> 114 <tests>
115 <test> 115 <test>