Mercurial > repos > iuc > stacks2_cstacks

comparison stacks_cstacks.xml @ 2:fcce77c09289 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/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
author iuc
date Thu, 16 Jul 2020 07:23:04 -0400
parents da351b9031de
children 0cd2df8af811
comparison
equal deleted inserted replaced
1:f4aab9196d1e 2:fcce77c09289
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="version_cmd"/> 7 <expand macro="version_cmd"/>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 #import re 9 #import re
10 10
11 mkdir stacks_inputs stacks_outputs 11 trap ">&2 cat '$output_log'" err exit &&
12 && 12 mkdir stacks_inputs stacks_outputs &&
13 13
14 @LINK_STACKS_INPUT@ 14 @LINK_STACKS_INPUT@
15
16 cstacks 15 cstacks
17 16
18 -p \${GALAXY_SLOTS:-1} 17 -p \${GALAXY_SLOTS:-1}
19 18
20 #if $popmap 19 #if $popmap
36 #if $k_len: 35 #if $k_len:
37 --k_len $k_len 36 --k_len $k_len
38 #end if 37 #end if
39 $report_mmatches 38 $report_mmatches
40 @TEE_APPEND_LOG@ 39 @TEE_APPEND_LOG@
41 @CAT_LOG_TO_STDERR@
42 40
43 #if $popmap 41 #if $popmap
44 ## When using a popmap, cstacks writes to the input dir 42 ## When using a popmap, cstacks writes to the input dir
45 && mv stacks_inputs/catalog.*.tsv stacks_outputs/ 43 && mv stacks_inputs/catalog.*.tsv stacks_outputs/
46 #end if 44 #end if
47
48 ]]></command> 45 ]]></command>
49 46
50 <inputs> 47 <inputs>
51 <expand macro="input_stacks_macro"/> 48 <expand macro="input_stacks_macro"/>
52 49
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" /> 50 <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 51
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)"/> 52 <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 53
57 <expand macro="gap_options"/> 54 <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"/> 55 <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" /> 56 <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"/> 57 <expand macro="in_log"/>
61 </inputs> 58 </inputs>
62 59
63 <outputs> 60 <outputs>
64 <expand macro="out_log"/> 61 <expand macro="out_log"/>
65 <expand macro="cstacks_outputs_macro"/> 62 <expand macro="cstacks_outputs_macro"/>
66 </outputs> 63 </outputs>
67 64
68 <tests> 65 <tests>
69 <!-- test w default options + popmap --> 66 <!-- test w default options + popmap -->
70 <test> 67 <test expect_num_outputs="2">
71 <param name="input_stacks"> 68 <param name="input_stacks">
72 <collection type="list"> 69 <collection type="list">
73 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" /> 70 <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" /> 71 <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" /> 72 <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" /> 73 <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" /> 74 <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" /> 75 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/>
79 </collection> 76 </collection>
80 </param> 77 </param>
81 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 78 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
82 <param name="add_log" value="yes" /> 79 <assert_command>
80 <has_text text="-M "/>
81 <has_text text="--max_gaps 2.0"/>
82 <has_text text="--min_aln_len 0.8"/>
83 </assert_command>
84 <param name="add_log" value="yes"/>
83 <output name="output_log" ftype="txt" file="cstacks/cstacks.log"/> 85 <output name="output_log" ftype="txt" file="cstacks/cstacks.log"/>
86 <!-- 1st test checks for file content allowing differences in the 2 comment lines that contain date and version -->
84 <output_collection name="catalog" type="list"> 87 <output_collection name="catalog" type="list">
85 <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="2"/> 88 <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="4"/>
86 <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="2" /> 89 <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="4"/>
87 <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="2" /> 90 <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="4"/>
88 </output_collection> 91 </output_collection>
89 </test> 92 </test>
90 <!-- test w default options --> 93 <!-- test w default options -->
91 <test> 94 <test expect_num_outputs="2">
92 <param name="input_stacks"> 95 <param name="input_stacks">
93 <collection type="list"> 96 <collection type="list">
94 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" /> 97 <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" /> 98 <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" /> 99 <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" /> 100 <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" /> 101 <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" /> 102 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/>
100 </collection> 103 </collection>
101 </param> 104 </param>
102 <param name="add_log" value="yes" /> 105 <assert_command>
103 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> 106 <not_has_text text="-M "/>
107 <has_text text="--max_gaps 2.0"/>
108 <has_text text="--min_aln_len 0.8"/>
109 </assert_command>
110 <param name="add_log" value="yes"/>
111 <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output>
104 <output_collection name="catalog" type="list"> 112 <output_collection name="catalog" type="list">
105 <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="2"/> 113 <element name="catalog.alleles"><assert_contents><has_text text="# cstacks completed on "/></assert_contents></element>
106 <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="2" /> 114 <element name="catalog.snps"><assert_contents><has_text text="# cstacks completed on "/></assert_contents></element>
107 <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="2" /> 115 <element name="catalog.tags"><assert_contents><has_text text="# cstacks completed on "/></assert_contents></element>
108 </output_collection> 116 </output_collection>
109 </test> 117 </test>
110 <!-- test w non default options (wo gapped, because tested already in ustacks) --> 118 <!-- test w non default options (wo gapped, because tested already in ustacks) -->
111 <test> 119 <test expect_num_outputs="1">
112 <param name="input_stacks"> 120 <param name="input_stacks">
113 <collection type="list"> 121 <collection type="list">
114 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" /> 122 <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" /> 123 <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" /> 124 <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" /> 125 <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" /> 126 <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" /> 127 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/>
120 </collection> 128 </collection>
121 </param> 129 </param>
122 <param name="n" value="2"/> 130 <param name="n" value="2"/>
123 <param name="k_len" value="23"/> 131 <param name="k_len" value="23"/>
124 <param name="report_mmatches" value="--report_mmatches" /> 132 <param name="report_mmatches" value="--report_mmatches"/>
125 <assert_command> 133 <assert_command>
126 <has_text text="--k_len 23" /> 134 <not_has_text text="-M "/>
127 <has_text text="-n 2" /> 135 <has_text text="--k_len 23"/>
128 <has_text text="--report_mmatches" /> 136 <has_text text="-n 2"/>
137 <has_text text="--report_mmatches"/>
129 </assert_command> 138 </assert_command>
130 <param name="add_log" value="yes" /> 139 <param name="add_log" value="no"/>
131 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> 140 <assert_stderr><has_text text="done."/></assert_stderr>
132 <output_collection name="catalog" type="list"> 141 <output_collection name="catalog" type="list">
133 <element name="catalog.alleles" file="cstacks/catalog.alleles.tsv" ftype="tabular" lines_diff="2"/> 142 <element name="catalog.alleles"><assert_contents><has_text text="# cstacks completed on "/></assert_contents></element>
134 <element name="catalog.snps" file="cstacks/catalog.snps.tsv" ftype="tabular" lines_diff="2" /> 143 <element name="catalog.snps"><assert_contents><has_text text="# cstacks completed on "/></assert_contents></element>
135 <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="2" /> 144 <element name="catalog.tags"><assert_contents><has_text text="# cstacks completed on "/></assert_contents></element>
136 </output_collection> 145 </output_collection>
137 </test> 146 </test>
138 </tests> 147 </tests>
139 <help> 148 <help>
140 <![CDATA[ 149 <![CDATA[
171 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ 180 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
172 181
173 @STACKS_INFOS@ 182 @STACKS_INFOS@
174 ]]> 183 ]]>
175 </help> 184 </help>
176 <expand macro="citation" /> 185 <expand macro="citation"/>
177 </tool> 186 </tool>