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comparison stacks_cstacks.xml @ 0:da351b9031de draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author iuc
date Mon, 01 Jul 2019 11:03:59 -0400
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children fcce77c09289
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-1:000000000000 0:da351b9031de
1 <tool id="stacks2_cstacks" name="Stacks2: cstacks" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
2 <description>Generate catalog of loci</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_cmd"/>
8 <command detect_errors="aggressive"><![CDATA[
9 #import re
10
11 mkdir stacks_inputs stacks_outputs
12 &&
13
14 @LINK_STACKS_INPUT@
15
16 cstacks
17
18 -p \${GALAXY_SLOTS:-1}
19
20 #if $popmap
21 -P stacks_inputs
22 -M '$popmap'
23 #else
24 #for $sample in $samples
25 -s 'stacks_inputs/$sample'
26 #end for
27 -o stacks_outputs
28 #end if
29
30 -n $n
31 ## -c not implemented in Galaxy (appending can be done in Galaxy)
32
33 @GAP_OPTIONS@
34
35 ## Advanced Options
36 #if $k_len:
37 --k_len $k_len
38 #end if
39 $report_mmatches
40 @TEE_APPEND_LOG@
41 @CAT_LOG_TO_STDERR@
42
43 #if $popmap
44 ## When using a popmap, cstacks writes to the input dir
45 && mv stacks_inputs/catalog.*.tsv stacks_outputs/
46 #end if
47
48 ]]></command>
49
50 <inputs>
51 <expand macro="input_stacks_macro"/>
52
53 <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, the catalog will be built from samples listed in this file" optional="true" argument="-M" />
54
55 <param argument="-n" type="integer" value="1" label="Number of mismatches allowed between sample loci when building the catalog" help="(default 1; suggested: set to ustacks -M)"/>
56
57 <expand macro="gap_options"/>
58 <param argument="--k_len" type="integer" min="5" max="31" value="" optional="true" label="K-mer size for matching between between catalog loci" help="default: automatic"/>
59 <param argument="--report_mmatches" type="boolean" checked="false" truevalue="--report_mmatches" falsevalue="" label="Report query loci that match more than one catalog locus" />
60 <expand macro="in_log"/>
61 </inputs>
62
63 <outputs>
64 <expand macro="out_log"/>
65 <expand macro="cstacks_outputs_macro"/>
66 </outputs>
67
68 <tests>
69 <!-- test w default options + popmap -->
70 <test>
71 <param name="input_stacks">
72 <collection type="list">
73 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
74 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
75 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
76 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
77 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
78 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
79 </collection>
80 </param>
81 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
82 <param name="add_log" value="yes" />
83 <output name="output_log" ftype="txt" file="cstacks/cstacks.log"/>
84 <output_collection name="catalog" type="list">
85 <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="2"/>
86 <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="2" />
87 <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="2" />
88 </output_collection>
89 </test>
90 <!-- test w default options -->
91 <test>
92 <param name="input_stacks">
93 <collection type="list">
94 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
95 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
96 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
97 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
98 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
99 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
100 </collection>
101 </param>
102 <param name="add_log" value="yes" />
103 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output>
104 <output_collection name="catalog" type="list">
105 <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="2"/>
106 <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="2" />
107 <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="2" />
108 </output_collection>
109 </test>
110 <!-- test w non default options (wo gapped, because tested already in ustacks) -->
111 <test>
112 <param name="input_stacks">
113 <collection type="list">
114 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
115 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
116 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
117 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
118 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
119 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
120 </collection>
121 </param>
122 <param name="n" value="2"/>
123 <param name="k_len" value="23"/>
124 <param name="report_mmatches" value="--report_mmatches" />
125 <assert_command>
126 <has_text text="--k_len 23" />
127 <has_text text="-n 2" />
128 <has_text text="--report_mmatches" />
129 </assert_command>
130 <param name="add_log" value="yes" />
131 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output>
132 <output_collection name="catalog" type="list">
133 <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="2"/>
134 <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="2" />
135 <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="2" />
136 </output_collection>
137 </test>
138 </tests>
139 <help>
140 <![CDATA[
141 .. class:: infomark
142
143 **What it does**
144
145 A catalog can be built from any set of samples processed by ustacks. It will create a set of consensus loci, merging alleles together. In the case of a genetic cross, a catalog would be constructed from the parents of the cross to create a set of all possible alleles expected in the progeny of the cross.
146
147 --------
148
149 **Input files**
150
151 Output from denovo_map or ustacks
152
153 **Output files**
154
155 - catalog.tags file:
156
157 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
158
159 Notes: For the tags file, each stack will start in the file with a consensus sequence for the entire stack followed by the flags for that stack. Then, each individual read that was merged into that stack will follow. The next stack will start with another consensus sequence.
160
161
162 - catalog.snps file:
163
164 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
165
166 Notes: If a stack has two SNPs called within it, then there will be two lines in this file listing each one.
167
168
169 - catalog.alleles file:
170
171 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
172
173 @STACKS_INFOS@
174 ]]>
175 </help>
176 <expand macro="citation" />
177 </tool>