Mercurial > repos > matthias > stacks2_sstacks

comparison stacks_sstacks.xml @ 4:176f2a0c6683 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 03:35:36 -0500
parents e0ac675a6785
children aef37afe214f
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3:e0ac675a6785 4:176f2a0c6683
68 && mv stacks_inputs/*matches.tsv stacks_outputs/ 68 && mv stacks_inputs/*matches.tsv stacks_outputs/
69 #end if 69 #end if
70 ]]></command> 70 ]]></command>
71 71
72 <inputs> 72 <inputs>
73 <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog files" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks" /> 73 <expand macro="input_cat_macro"/>
74 <param name="input_tags" format="tabular,txt" type="data_collection" collection_type="list" label="Samples stacks" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks/pstacks" /> 74 <expand macro="input_tags_macro"/>
75 75
76 <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" /> 76 <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" />
77 <param argument="-x" type="boolean" checked="false" truevalue="-x" falsevalue="" label="don't verify haplotype of matching locus" /> 77 <param argument="-x" type="boolean" checked="false" truevalue="-x" falsevalue="" label="don't verify haplotype of matching locus" />
78 <expand macro="gap_options_onoff"/> 78 <expand macro="gap_options_onoff"/>
79 <expand macro="in_log"/> 79 <expand macro="in_log"/>
161 <![CDATA[ 161 <![CDATA[
162 .. class:: infomark 162 .. class:: infomark
163 163
164 **What it does** 164 **What it does**
165 165
166 Sets of stacks constructed by the ustacks or pstacks programs 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. 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.
167 167
168 -------- 168 --------
169 169
170 **Input files** 170 **Input files**
171 171
172 Output from denovo_map, refmap or cstacks/ustacks/pstacks 172 Output from denovo_map, refmap or cstacks/ustack
173 173
174 **Output files** 174 **Output files**
175 175
176 - XXX.tags.tsv file: 176 - XXX.tags.tsv file:
177 177