Mercurial > repos > iuc > stacks2_sstacks

comparison stacks_sstacks.xml @ 2:0b8c84a7fdb5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
author iuc
date Wed, 15 Jul 2020 17:20:51 -0400
parents e58e2ecb6285
children 09b8edb56d80
comparison
equal deleted inserted replaced
1:e58e2ecb6285 2:0b8c84a7fdb5
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 &&
14 13
15 @LINK_STACKS_INPUT@ 14 @LINK_STACKS_INPUT@
16 @LINK_CAT_INPUT@ 15 @LINK_CAT_INPUT@
17 16
18 sstacks 17 sstacks
32 31
33 $x 32 $x
34 33
35 @GAP_OPTIONS_ONOFF@ 34 @GAP_OPTIONS_ONOFF@
36 @TEE_APPEND_LOG@ 35 @TEE_APPEND_LOG@
37 @CAT_LOG_TO_STDERR@
38 36
39 #if $popmap 37 #if $popmap
40 ## When using a popmap, stacks write to the input dir 38 ## When using a popmap, stacks write to the input dir
41 && mv stacks_inputs/*matches.tsv stacks_outputs/ 39 && mv stacks_inputs/*matches.tsv stacks_outputs/
42 #end if 40 #end if
43 ]]></command> 41 ]]></command>
44 42
45 <inputs> 43 <inputs>
46 <expand macro="input_stacks_macro"/> 44 <expand macro="input_stacks_macro"/>
47 <expand macro="input_cat_macro"/> 45 <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" /> 46 <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" /> 47 <param argument="-x" type="boolean" checked="true" truevalue="" falsevalue="-x" label="Verify haplotype of matching locus"/>
50 <expand macro="gap_options_onoff"/> 48 <expand macro="gap_options_onoff"/>
51 <expand macro="in_log"/> 49 <expand macro="in_log"/>
52 </inputs> 50 </inputs>
53 51
54 <outputs> 52 <outputs>
56 <expand macro="sstacks_outputs_macro"/> 54 <expand macro="sstacks_outputs_macro"/>
57 </outputs> 55 </outputs>
58 56
59 <tests> 57 <tests>
60 <!-- test w default parameters and popmap --> 58 <!-- test w default parameters and popmap -->
61 <test> 59 <test expect_num_outputs="2">
62 <param name="input_cat"> 60 <param name="input_cat">
63 <collection type="list"> 61 <collection type="list">
64 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" /> 62 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/>
65 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" /> 63 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/>
66 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" /> 64 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/>
67 </collection> 65 </collection>
68 </param> 66 </param>
69 <param name="input_stacks"> 67 <param name="input_stacks">
70 <collection type="list"> 68 <collection type="list">
71 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" /> 69 <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" /> 70 <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" /> 71 <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" /> 72 <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" /> 73 <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" /> 74 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/>
77 </collection> 75 </collection>
78 </param> 76 </param>
79 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 77 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
80 <param name="add_log" value="yes" /> 78 <param name="add_log" value="yes"/>
81 <assert_command> 79 <assert_command>
82 <not_has_text text="-x" /> 80 <not_has_text text="-x"/>
83 <not_has_text text="--disable-gapped" /> 81 <not_has_text text="--disable-gapped"/>
84 <has_text text="-M" /> 82 <has_text text="-M"/>
85 </assert_command> 83 </assert_command>
86 <output name="output_log" ftype="txt" file="sstacks/sstacks.log"/> 84 <output name="output_log" ftype="txt" file="sstacks/sstacks.log"/>
87 <output_collection name="matches" type="list"> 85 <output_collection name="matches" type="list">
88 <element name="PopA_01.matches" file="sstacks/PopA_01.matches.tsv" ftype="tabular" lines_diff="2"/> 86 <element name="PopA_01.matches" file="sstacks/PopA_01.matches.tsv" ftype="tabular" lines_diff="4"/>
89 <element name="PopA_02.matches" file="sstacks/PopA_02.matches.tsv" ftype="tabular" lines_diff="2"/> 87 <element name="PopA_02.matches" file="sstacks/PopA_02.matches.tsv" ftype="tabular" lines_diff="4"/>
90 </output_collection> 88 </output_collection>
91 </test> 89 </test>
92 <!-- test w default parameters --> 90 <!-- test w default parameters -->
93 <test> 91 <test expect_num_outputs="2">
94 <param name="input_cat"> 92 <param name="input_cat">
95 <collection type="list"> 93 <collection type="list">
96 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" /> 94 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/>
97 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" /> 95 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/>
98 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" /> 96 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/>
99 </collection> 97 </collection>
100 </param> 98 </param>
101 <param name="input_stacks"> 99 <param name="input_stacks">
102 <collection type="list"> 100 <collection type="list">
103 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" /> 101 <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" /> 102 <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" /> 103 <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" /> 104 <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" /> 105 <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" /> 106 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/>
109 </collection> 107 </collection>
110 </param> 108 </param>
111 <param name="add_log" value="yes" /> 109 <param name="add_log" value="yes"/>
112 <assert_command> 110 <assert_command>
113 <not_has_text text="-x" /> 111 <not_has_text text="-x"/>
114 <not_has_text text="--disable-gapped" /> 112 <not_has_text text="--disable-gapped"/>
115 <not_has_text text="-M" /> 113 <not_has_text text="-M"/>
116 </assert_command> 114 </assert_command>
117 <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output> 115 <output name="output_log" ftype="txt"><assert_contents><has_text text="done."/></assert_contents></output>
118 <output_collection name="matches" type="list" count="2"> 116 <output_collection name="matches" type="list" count="2">
119 <element name="PopA_01.matches"><assert_contents><has_text text="generated on " /></assert_contents></element> 117 <element name="PopA_01.matches"><assert_contents><has_text text="# sstacks completed on "/></assert_contents></element>
120 <element name="PopA_02.matches"><assert_contents><has_text text="generated on " /></assert_contents></element> 118 <element name="PopA_02.matches"><assert_contents><has_text text="# sstacks completed on "/></assert_contents></element>
121 </output_collection> 119 </output_collection>
122 </test> 120 </test>
123 121
124 <!-- test w non default parameters and popmap--> 122 <!-- test w non default parameters and popmap-->
125 <test> 123 <test expect_num_outputs="1">
126 <param name="input_cat"> 124 <param name="input_cat">
127 <collection type="list"> 125 <collection type="list">
128 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" /> 126 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/>
129 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" /> 127 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/>
130 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" /> 128 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/>
131 </collection> 129 </collection>
132 </param> 130 </param>
133 <param name="input_stacks"> 131 <param name="input_stacks">
134 <collection type="list"> 132 <collection type="list">
135 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" /> 133 <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" /> 134 <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" /> 135 <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" /> 136 <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" /> 137 <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" /> 138 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/>
141 </collection> 139 </collection>
142 </param> 140 </param>
143 <param name="gapped|use_gapped" value="yes" /> 141 <param name="gapped|use_gapped" value="yes"/>
144 <param name="x" value="-x" /> 142 <param name="x" value="-x"/>
145 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 143 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
146 <param name="add_log" value="yes" /> 144 <param name="add_log" value="no"/>
147 <assert_command> 145 <assert_command>
148 <has_text text="-x" /> 146 <has_text text="-x"/>
149 <not_has_text text="--disable-gapped" /> 147 <not_has_text text="--disable-gapped"/>
150 <has_text text="-M" /> 148 <has_text text="-M"/>
151 </assert_command> 149 </assert_command>
152 <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output> 150 <assert_stderr><has_text text="done."/></assert_stderr>
153 <output_collection name="matches" type="list" count="2"> 151 <output_collection name="matches" type="list" count="2">
154 <element name="PopA_01.matches"><assert_contents><has_text text="generated on " /></assert_contents></element> 152 <element name="PopA_01.matches"><assert_contents><has_text text="# sstacks completed on "/></assert_contents></element>
155 <element name="PopA_02.matches"><assert_contents><has_text text="generated on " /></assert_contents></element> 153 <element name="PopA_02.matches"><assert_contents><has_text text="# sstacks completed on "/></assert_contents></element>
156 </output_collection> 154 </output_collection>
157 </test> 155 </test>
158 </tests> 156 </tests>
159 157
160 <help> 158 <help>
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. 196 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.
199 197
200 @STACKS_INFOS@ 198 @STACKS_INFOS@
201 ]]> 199 ]]>
202 </help> 200 </help>
203 <expand macro="citation" /> 201 <expand macro="citation"/>
204 </tool> 202 </tool>