Mercurial > repos > iuc > stacks_cstacks

comparison stacks_cstacks.xml @ 3:6a7c5e218732 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 17:28:35 -0400
parents a1807de3995a
children a62f7e799494
comparison
equal deleted inserted replaced
2:5bd1418f4227 3:6a7c5e218732
1 <tool id="stacks_cstacks" name="Stacks: cstacks" version="@WRAPPER_VERSION@.0"> 1 <tool id="stacks_cstacks" name="Stacks: cstacks" version="@WRAPPER_VERSION@.2">
2 <description>build a catalogue of loci</description> 2 <description>build a catalogue of loci</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"/>
12 12
13 && 13 &&
14 14
15 #set $samples = "" 15 #set $samples = ""
16 #for $input_file in $input_col: 16 #for $input_file in $input_col:
17 #set $filename = str($input_file.name) 17 #set $filename = str($input_file.element_identifier)
18 #if not filename.endswith('.tsv'): 18 #if not filename.endswith('.tsv'):
19 #set $filename = ".tsv" 19 #set $filename = $filename + ".tsv"
20 #end if 20 #end if
21 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename): 21 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename):
22 ln -s "${input_file}" "stacks_inputs/$filename" && 22 ln -s "${input_file}" "stacks_inputs/$filename" &&
23 23
24 #if $filename.endswith('.tags.tsv'): 24 #if $filename.endswith('.tags.tsv'):
47 --max_gaps $gapped.max_gaps 47 --max_gaps $gapped.max_gaps
48 --min_aln_len $gapped.min_aln_len 48 --min_aln_len $gapped.min_aln_len
49 #end if 49 #end if
50 50
51 -o stacks_outputs 51 -o stacks_outputs
52
53 > cstacks.log 2>&1
52 ]]></command> 54 ]]></command>
53 55
54 <inputs> 56 <inputs>
55 <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map, refmap, ustacks or pstacks)" /> 57 <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map, refmap, ustacks or pstacks)" />
56 58
69 </when> 71 </when>
70 </conditional> 72 </conditional>
71 </inputs> 73 </inputs>
72 74
73 <outputs> 75 <outputs>
76 <data format="txt" name="output_log" label="cstacks.log with ${tool.name} on ${on_string}" from_work_dir="cstacks.log" />
77
74 <data format="tabular" name="catalogtags" label="Catalog assembled loci (tags) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.tags.tsv" /> 78 <data format="tabular" name="catalogtags" label="Catalog assembled loci (tags) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.tags.tsv" />
75 <data format="tabular" name="catalogsnps" label="Catalog model calls (snps) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.snps.tsv" /> 79 <data format="tabular" name="catalogsnps" label="Catalog model calls (snps) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.snps.tsv" />
76 <data format="tabular" name="catalogalleles" label="Catalog haplotypes (alleles) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.alleles.tsv" /> 80 <data format="tabular" name="catalogalleles" label="Catalog haplotypes (alleles) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.alleles.tsv" />
77 </outputs> 81 </outputs>
78 82
92 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" /> 96 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
93 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" /> 97 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
94 </collection> 98 </collection>
95 </param> 99 </param>
96 100
101 <output name="output_log">
102 <assert_contents>
103 <has_text text="done." />
104 </assert_contents>
105 </output>
106
97 <!-- catalog --> 107 <!-- catalog -->
98 <output name="catalogtags"> 108 <output name="catalogtags">
99 <assert_contents> 109 <assert_contents>
100 <has_text text="catalog generated on" /> 110 <has_text text="catalog generated on" />
101 </assert_contents> 111 </assert_contents>
128 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" /> 138 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
129 </collection> 139 </collection>
130 </param> 140 </param>
131 <param name="gapped|use_gapped" value="true" /> 141 <param name="gapped|use_gapped" value="true" />
132 142
143 <output name="output_log">
144 <assert_contents>
145 <has_text text="done." />
146 </assert_contents>
147 </output>
148
133 <!-- catalog --> 149 <!-- catalog -->
134 <output name="catalogtags"> 150 <output name="catalogtags">
135 <assert_contents> 151 <assert_contents>
136 <has_text text="catalog generated on" /> 152 <has_text text="catalog generated on" />
137 </assert_contents> 153 </assert_contents>