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comparison stacks_cstacks.xml @ 3:61afc5a3cd8e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c42d129928cfd153ba7a922368c8e76e79b242b2
author matthias
date Fri, 04 Jan 2019 03:31:18 -0500
parents d31714d7f03e
children 924e7889aa05
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equal deleted inserted replaced
2:8427e904f352 3:61afc5a3cd8e
17 ## present catalogs are ignored) 17 ## present catalogs are ignored)
18 ## link name is element_identifier(.tsv) 18 ## link name is element_identifier(.tsv)
19 ## - create -s sample1prefix -s sample2prefix .. 19 ## - create -s sample1prefix -s sample2prefix ..
20 20
21 #set $samples = "" 21 #set $samples = ""
22 #for $input_file in $input_col 22 #for $input_file in $input_cat
23 #set $filename = str($input_file.element_identifier) 23 #set $filename = str($input_file.element_identifier)
24 #if not filename.endswith('.tsv') 24 #if not filename.endswith('.tsv')
25 #set $filename = $filename + ".tsv" 25 #set $filename = $filename + ".tsv"
26 #end if 26 #end if
27 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename) 27 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename)
64 #end if 64 #end if
65 65
66 ]]></command> 66 ]]></command>
67 67
68 <inputs> 68 <inputs>
69 <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map, refmap, ustacks or pstacks)" /> 69 <expand macro="input_cat_macro"/>
70 70
71 <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" /> 71 <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" />
72 72
73 <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)"/> 73 <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)"/>
74 74
85 85
86 <tests> 86 <tests>
87 <!-- TODO add test w popmap --> 87 <!-- TODO add test w popmap -->
88 <!-- test w default options --> 88 <!-- test w default options -->
89 <test> 89 <test>
90 <param name="input_col"> 90 <param name="input_cat">
91 <collection type="list"> 91 <collection type="list">
92 <element name="PopA_01.alleles.tsv" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" /> 92 <element name="PopA_01.alleles.tsv" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
93 <element name="PopA_01.snps.tsv" ftype="tabular" value="ustacks/PopA_01.snps.tsv" /> 93 <element name="PopA_01.snps.tsv" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
94 <element name="PopA_01.tags.tsv" ftype="tabular" value="ustacks/PopA_01.tags.tsv" /> 94 <element name="PopA_01.tags.tsv" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
95 <element name="PopA_02.alleles.tsv" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" /> 95 <element name="PopA_02.alleles.tsv" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
105 <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="2" /> 105 <element name="catalog.tags" file="cstacks/catalog.tags.tsv" ftype="tabular" lines_diff="2" />
106 </output_collection> 106 </output_collection>
107 </test> 107 </test>
108 <!-- test w non default options (wo gapped, because tested already in ustacks) --> 108 <!-- test w non default options (wo gapped, because tested already in ustacks) -->
109 <test> 109 <test>
110 <param name="input_col"> 110 <param name="input_cat">
111 <collection type="list"> 111 <collection type="list">
112 <element name="PopA_01.alleles.tsv" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" /> 112 <element name="PopA_01.alleles.tsv" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
113 <element name="PopA_01.snps.tsv" ftype="tabular" value="ustacks/PopA_01.snps.tsv" /> 113 <element name="PopA_01.snps.tsv" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
114 <element name="PopA_01.tags.tsv" ftype="tabular" value="ustacks/PopA_01.tags.tsv" /> 114 <element name="PopA_01.tags.tsv" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
115 <element name="PopA_02.alleles.tsv" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" /> 115 <element name="PopA_02.alleles.tsv" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
138 <![CDATA[ 138 <![CDATA[
139 .. class:: infomark 139 .. class:: infomark
140 140
141 **What it does** 141 **What it does**
142 142
143 A catalog can be built from any set of samples processed by the ustacks or pstacks programs. 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. 143 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.
144 144
145 -------- 145 --------
146 146
147 **Input files** 147 **Input files**
148 148
149 Output from denovo_map, refmap, ustacks or pstacks 149 Output from denovo_map, refmap, or ustacks
150 150
151 **Output files** 151 **Output files**
152 152
153 - XXX.tags.tsv file: 153 - XXX.tags.tsv file:
154 154