Mercurial > repos > iuc > stacks_pstacks

comparison stacks_pstacks.xml @ 3:fede8a808d36 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 17:27:31 -0400
parents 0146d9d89e21
children 77e29e6a6101
comparison
equal deleted inserted replaced
2:0f16a6c30085 3:fede8a808d36
1 <tool id="stacks_pstacks" name="Stacks: pstacks" version="@WRAPPER_VERSION@.0"> 1 <tool id="stacks_pstacks" name="Stacks: pstacks" version="@WRAPPER_VERSION@.2">
2 <description>find stacks from short reads mapped to a reference genome</description> 2 <description>find stacks from short reads mapped to a reference genome</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 mkdir stacks_inputs stacks_outputs 12 mkdir stacks_inputs stacks_outputs
13 13
14 && 14 &&
15 15
16 #if $sample.ext == "sam": 16 #if $sample.ext == "sam":
17 #set $data_path = splitext($sample.name)[0] 17 #set $data_path = splitext($sample.element_identifier)[0]
18 #set $data_path = re.sub(r'\.1$', '', $data_path) 18 #set $data_path = re.sub(r'\.1$', '', $data_path)
19 #set $data_path = "stacks_inputs/" + $data_path + ".sam" 19 #set $data_path = "stacks_inputs/" + $data_path + ".sam"
20 #set inputype = "sam" 20 #set inputype = "sam"
21 #else: 21 #else:
22 #set $data_path = splitext($sample.name)[0] 22 #set $data_path = splitext($sample.element_identifier)[0]
23 #set $data_path = re.sub(r'\.1$', '', $data_path) 23 #set $data_path = re.sub(r'\.1$', '', $data_path)
24 #set $data_path = "stacks_inputs/" + $data_path + ".bam" 24 #set $data_path = "stacks_inputs/" + $data_path + ".bam"
25 #set inputype = "bam" 25 #set inputype = "bam"
26 #end if 26 #end if
27 27
56 --bc_err_freq $bc_err_freq 56 --bc_err_freq $bc_err_freq
57 #end if 57 #end if
58 58
59 -o stacks_outputs 59 -o stacks_outputs
60 60
61 > pstacks.log 2>&1
62
61 ## If input is in bam format, stacks will output gzipped files (no option to control this) 63 ## If input is in bam format, stacks will output gzipped files (no option to control this)
62 && gunzip stacks_outputs/*.gz 64 && if ls stacks_outputs/*.gz > /dev/null 2>&1; then gunzip stacks_outputs/*.gz; fi
63 ]]></command> 65 ]]></command>
64 66
65 <inputs> 67 <inputs>
66 <param name="sample" argument="-f" format="fastqsanger,fasta" type="data" label="Input short reads from an individual" /> 68 <param name="sample" argument="-f" format="fastqsanger,fasta" type="data" label="Input short reads from an individual" />
67 69
75 <expand macro="snp_options_full"/> 77 <expand macro="snp_options_full"/>
76 </section> 78 </section>
77 </inputs> 79 </inputs>
78 80
79 <outputs> 81 <outputs>
82 <data format="txt" name="output_log" label="pstacks.log with ${tool.name} on ${on_string}" from_work_dir="pstacks.log" />
83
80 <collection name="tabs" type="list" label="Stacks from ${on_string}"> 84 <collection name="tabs" type="list" label="Stacks from ${on_string}">
81 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv" ext="tabular" directory="stacks_outputs" /> 85 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
82 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv" ext="tabular" directory="stacks_outputs" />> 86 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />>
83 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv" ext="tabular" directory="stacks_outputs" /> 87 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
84 <discover_datasets pattern="(?P&lt;name&gt;.+\.models)\.tsv" ext="tabular" directory="stacks_outputs" /> 88 <discover_datasets pattern="(?P&lt;name&gt;.+\.models)\.tsv$" ext="tabular" directory="stacks_outputs" />
85 </collection> 89 </collection>
86 </outputs> 90 </outputs>
87 91
88 <tests> 92 <tests>
89 <test> 93 <test>
90 <param name="sample" value="refmap/PopA_01.bam" ftype="bam" /> 94 <param name="sample" value="refmap/PopA_01.bam" ftype="bam" />
91 <param name="sample_id" value="4" /> 95 <param name="sample_id" value="4" />
96
97 <output name="output_log">
98 <assert_contents>
99 <has_text text="done." />
100 </assert_contents>
101 </output>
92 102
93 <output_collection name="tabs"> 103 <output_collection name="tabs">
94 <element name="PopA_01.tags"> 104 <element name="PopA_01.tags">
95 <assert_contents> 105 <assert_contents>
96 <has_text text="generated on " /> 106 <has_text text="generated on " />