Mercurial > repos > iuc > stacks_ustacks

comparison stacks_ustacks.xml @ 3:216c469422d2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
author iuc
date Sat, 25 Jun 2016 17:28:03 -0400
parents 7c5004f8cd49
children ff04b3748654
comparison
equal deleted inserted replaced
2:c2e3eca527c2 3:216c469422d2
1 <tool id="stacks_ustacks" name="Stacks: ustacks" version="@WRAPPER_VERSION@.0"> 1 <tool id="stacks_ustacks" name="Stacks: ustacks" version="@WRAPPER_VERSION@.1">
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"/>
12 mkdir stacks_inputs stacks_outputs 12 mkdir stacks_inputs stacks_outputs
13 13
14 && 14 &&
15 15
16 #if $sample.ext == "fastqsanger": 16 #if $sample.ext == "fastqsanger":
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 + ".fq" 19 #set $data_path = "stacks_inputs/" + $data_path + ".fq"
20 #set inputype = "fastq" 20 #set inputype = "fastq"
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 + ".fa" 24 #set $data_path = "stacks_inputs/" + $data_path + ".fa"
25 #set inputype = "fasta" 25 #set inputype = "fasta"
26 #end if 26 #end if
27 27
72 --model_type fixed 72 --model_type fixed
73 --bc_err_freq $bc_err_freq 73 --bc_err_freq $bc_err_freq
74 #end if 74 #end if
75 75
76 -o stacks_outputs 76 -o stacks_outputs
77
78 > ustacks.log 2>&1
77 ]]></command> 79 ]]></command>
78 80
79 <inputs> 81 <inputs>
80 <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" />
81 83
107 <expand macro="snp_options_full"/> 109 <expand macro="snp_options_full"/>
108 </section> 110 </section>
109 </inputs> 111 </inputs>
110 112
111 <outputs> 113 <outputs>
114 <data format="txt" name="output_log" label="ustacks.log with ${tool.name} on ${on_string}" from_work_dir="ustacks.log" />
115
112 <collection name="tabs" type="list" label="Stacks from ${on_string}"> 116 <collection name="tabs" type="list" label="Stacks from ${on_string}">
113 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv" ext="tabular" directory="stacks_outputs" /> 117 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
114 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv" ext="tabular" directory="stacks_outputs" />> 118 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />>
115 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv" ext="tabular" directory="stacks_outputs" /> 119 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
116 <discover_datasets pattern="(?P&lt;name&gt;.+\.models)\.tsv" ext="tabular" directory="stacks_outputs" /> 120 <discover_datasets pattern="(?P&lt;name&gt;.+\.models)\.tsv$" ext="tabular" directory="stacks_outputs" />
117 </collection> 121 </collection>
118 </outputs> 122 </outputs>
119 123
120 <tests> 124 <tests>
121 <test> 125 <test>
122 <param name="sample" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" /> 126 <param name="sample" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
123 <param name="sample_id" value="4" /> 127 <param name="sample_id" value="4" />
128
129 <output name="output_log">
130 <assert_contents>
131 <has_text text="done." />
132 </assert_contents>
133 </output>
124 134
125 <output_collection name="tabs"> 135 <output_collection name="tabs">
126 <element name="PopA_01.tags"> 136 <element name="PopA_01.tags">
127 <assert_contents> 137 <assert_contents>
128 <has_text text="generated on " /> 138 <has_text text="generated on " />