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comparison stacks_sstacks.xml @ 0:b7babdb3c219 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 11:01:59 -0400
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children e58e2ecb6285
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-1:000000000000 0:b7babdb3c219
1 <tool id="stacks2_sstacks" name="Stacks2: sstacks" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
2 <description>Match samples to the catalog</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
15 @LINK_STACKS_INPUT@
16 @LINK_CAT_INPUT@
17
18 sstacks
19
20 -p \${GALAXY_SLOTS:-1}
21
22 #if $popmap
23 -P stacks_inputs
24 -M '$popmap'
25 #else
26 -c stacks_inputs/
27 #for $sample in $samples
28 -s 'stacks_inputs/$sample'
29 #end for
30 -o stacks_outputs
31 #end if
32
33 $x
34
35 @GAP_OPTIONS_ONOFF@
36 @TEE_APPEND_LOG@
37 @CAT_LOG_TO_STDERR@
38
39 #if $popmap
40 ## When using a popmap, stacks write to the input dir
41 && mv stacks_inputs/*matches.tsv stacks_outputs/
42 #end if
43 ]]></command>
44
45 <inputs>
46 <expand macro="input_stacks_macro"/>
47 <expand macro="input_cat_macro"/>
48 <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M" />
49 <param argument="-x" type="boolean" checked="true" truevalue="" falsevalue="-x" label="Verify haplotype of matching locus" />
50 <expand macro="gap_options_onoff"/>
51 <expand macro="in_log"/>
52 </inputs>
53
54 <outputs>
55 <expand macro="out_log"/>
56 <expand macro="sstacks_outputs_macro"/>
57 </outputs>
58
59 <tests>
60 <!-- test w default parameters and popmap -->
61 <test>
62 <param name="input_cat">
63 <collection type="list">
64 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" />
65 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" />
66 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" />
67 </collection>
68 </param>
69 <param name="input_stacks">
70 <collection type="list">
71 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
72 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
73 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
74 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
75 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
76 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
77 </collection>
78 </param>
79 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
80 <param name="add_log" value="yes" />
81 <assert_command>
82 <not_has_text text="-x" />
83 <not_has_text text="--disable-gapped" />
84 <not_has_text text="-M" />
85 </assert_command>
86 <output name="output_log" ftype="txt" file="sstacks/sstacks.log"/>
87 <output_collection name="matches" type="list">
88 <element name="PopA_01.matches" file="sstacks/PopA_01.matches.tsv" ftype="tabular" lines_diff="2"/>
89 <element name="PopA_02.matches" file="sstacks/PopA_02.matches.tsv" ftype="tabular" lines_diff="2"/>
90 </output_collection>
91 </test>
92 <!-- test w default parameters -->
93 <test>
94 <param name="input_cat">
95 <collection type="list">
96 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" />
97 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" />
98 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" />
99 </collection>
100 </param>
101 <param name="input_stacks">
102 <collection type="list">
103 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
104 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
105 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
106 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
107 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
108 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
109 </collection>
110 </param>
111 <param name="add_log" value="yes" />
112 <assert_command>
113 <not_has_text text="-x" />
114 <not_has_text text="--disable-gapped" />
115 <not_has_text text="-M" />
116 </assert_command>
117 <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output>
118 <output_collection name="matches" type="list" count="2">
119 <element name="PopA_01.matches"><assert_contents><has_text text="generated on " /></assert_contents></element>
120 <element name="PopA_02.matches"><assert_contents><has_text text="generated on " /></assert_contents></element>
121 </output_collection>
122 </test>
123
124 <!-- test w non default parameters and popmap-->
125 <test>
126 <param name="input_cat">
127 <collection type="list">
128 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" />
129 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" />
130 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" />
131 </collection>
132 </param>
133 <param name="input_stacks">
134 <collection type="list">
135 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
136 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
137 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
138 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
139 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
140 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
141 </collection>
142 </param>
143 <param name="gapped|use_gapped" value="yes" />
144 <param name="x" value="-x" />
145 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
146 <param name="add_log" value="yes" />
147 <assert_command>
148 <has_text text="-x" />
149 <has_text text="--disable-gapped" />
150 <has_text text="-M" />
151 </assert_command>
152 <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output>
153 <output_collection name="matches" type="list" count="2">
154 <element name="PopA_01.matches"><assert_contents><has_text text="generated on " /></assert_contents></element>
155 <element name="PopA_02.matches"><assert_contents><has_text text="generated on " /></assert_contents></element>
156 </output_collection>
157 </test>
158 </tests>
159
160 <help>
161 <![CDATA[
162 .. class:: infomark
163
164 **What it does**
165
166 Sets of stacks constructed by ustacks can be searched against a catalog produced by cstacks. In the case of a genetic map, stacks from the progeny would be matched against the catalog to determine which progeny contain which parental alleles.
167
168 --------
169
170 **Input files**
171
172 Output from denovo_map, refmap or cstacks/ustack
173
174 **Output files**
175
176 - XXX.tags.tsv file:
177
178 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
179
180 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.
181
182
183 - XXX.snps.tsv file:
184
185 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
186
187 Notes: If a stack has two SNPs called within it, then there will be two lines in this file listing each one.
188
189
190 - XXX.alleles.tsv file:
191
192 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
193
194 - XXX.matches.tsv file:
195
196 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
197
198 Notes: Each line in this file records a match between a catalog locus and a locus in an individual, for a particular haplotype. The Batch ID plus the Catalog ID together represent a unique locus in the entire population, while the Sample ID and the Stack ID together represent a unique locus in an individual sample.
199
200 @STACKS_INFOS@
201 ]]>
202 </help>
203 <expand macro="citation" />
204 </tool>