Mercurial > repos > matthias > stacks2_sstacks
diff stacks_sstacks.xml @ 5:aef37afe214f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
| author | matthias |
|---|---|
| date | Wed, 27 Feb 2019 09:58:12 -0500 |
| parents | 176f2a0c6683 |
| children |
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--- a/stacks_sstacks.xml Fri Jan 04 03:35:36 2019 -0500 +++ b/stacks_sstacks.xml Wed Feb 27 09:58:12 2019 -0500 @@ -1,48 +1,19 @@ -<tool id="stacks2_sstacks" name="Stacks2: sstacks" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@"> - <description>match stacks to a catalog</description> +<tool id="stacks2_sstacks" name="Stacks2: sstacks" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@"> + <description>Match samples to the catalog</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> - <expand macro="stdio"/> - <command><![CDATA[ + <expand macro="version_cmd"/> + <command detect_errors="aggressive"><![CDATA[ #import re mkdir stacks_inputs stacks_outputs && -## TODO make sure that there is only a single catalog? -#set $catalog = "" -#for $input_file in $input_cat - #set $filename = str($input_file.element_identifier) - #if not filename.endswith('.tsv') - #set $filename = $filename + ".tsv" - #end if - ## TODO may be confused by catalog.calls from gstacks (maybe make .tsv not optional) - #if re.search('catalog\.[a-z]+(\.tsv)?$', $filename) - ln -s '${input_file}' 'stacks_inputs/$filename' && - - #if $filename.endswith('.tags.tsv') - #set catalog += " -c 'stacks_inputs/'" - #end if - #end if -#end for - -#set $samples = "" -#for $input_file in $input_tags - #set $filename = str($input_file.element_identifier) - #if not filename.endswith('.tsv') - #set $filename = $filename + ".tsv" - #end if - #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename) - ln -s '${input_file}' 'stacks_inputs/$filename' && - - #if $filename.endswith('.tags.tsv') - #set samples += " -s 'stacks_inputs/"+$filename[:-9] + "'" - #end if - #end if -#end for +@LINK_STACKS_INPUT@ +@LINK_CAT_INPUT@ sstacks @@ -52,15 +23,17 @@ -P stacks_inputs -M '$popmap' #else - $catalog - $samples + -c stacks_inputs/ + #for $sample in $samples + -s 'stacks_inputs/$sample' + #end for -o stacks_outputs #end if $x @GAP_OPTIONS_ONOFF@ -@TEE_APPEND_LOG@ +@TEE_APPEND_LOG@ @CAT_LOG_TO_STDERR@ #if $popmap @@ -70,11 +43,10 @@ ]]></command> <inputs> - <expand macro="input_cat_macro"/> - <expand macro="input_tags_macro"/> - + <expand macro="input_stacks_macro"/> + <expand macro="input_cat_macro"/> <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" /> - <param argument="-x" type="boolean" checked="false" truevalue="-x" falsevalue="" label="don't verify haplotype of matching locus" /> + <param argument="-x" type="boolean" checked="true" truevalue="" falsevalue="-x" label="Verify haplotype of matching locus" /> <expand macro="gap_options_onoff"/> <expand macro="in_log"/> </inputs> @@ -85,27 +57,26 @@ </outputs> <tests> - <!-- test w default parameters --> + <!-- test w default parameters and popmap --> <test> <param name="input_cat"> <collection type="list"> - <element name="catalog.alleles.tsv" ftype="tabular" value="cstacks/catalog.alleles.tsv" /> - <element name="catalog.snps.tsv" ftype="tabular" value="cstacks/catalog.snps.tsv" /> - <element name="catalog.tags.tsv" ftype="tabular" value="cstacks/catalog.tags.tsv" /> + <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" /> + <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" /> + <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" /> </collection> </param> - <param name="input_tags"> + <param name="input_stacks"> <collection type="list"> - <element name="PopA_01.alleles.tsv" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" /> - <!-- TODO add test with results from full previous denovomap output also in cstacks <element name="PopA_01.matches.tsv" ftype="tabular" value="ustacks/PopA_01.matches.tsv" />--> - <element name="PopA_01.snps.tsv" ftype="tabular" value="ustacks/PopA_01.snps.tsv" /> - <element name="PopA_01.tags.tsv" ftype="tabular" value="ustacks/PopA_01.tags.tsv" /> - <element name="PopA_02.alleles.tsv" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" /> - <!-- <element name="PopA_02.matches.tsv" ftype="tabular" value="ustacks/PopA_02.matches.tsv" />--> - <element name="PopA_02.snps.tsv" ftype="tabular" value="ustacks/PopA_02.snps.tsv" /> - <element name="PopA_02.tags.tsv" ftype="tabular" value="ustacks/PopA_02.tags.tsv" /> + <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" /> + <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" /> + <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" /> + <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" /> + <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" /> + <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" /> </collection> </param> + <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> <param name="add_log" value="yes" /> <assert_command> <not_has_text text="-x" /> @@ -118,26 +89,55 @@ <element name="PopA_02.matches" file="sstacks/PopA_02.matches.tsv" ftype="tabular" lines_diff="2"/> </output_collection> </test> + <!-- test w default parameters --> + <test> + <param name="input_cat"> + <collection type="list"> + <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" /> + <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" /> + <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" /> + </collection> + </param> + <param name="input_stacks"> + <collection type="list"> + <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" /> + <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" /> + <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" /> + <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" /> + <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" /> + <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" /> + </collection> + </param> + <param name="add_log" value="yes" /> + <assert_command> + <not_has_text text="-x" /> + <not_has_text text="--disable-gapped" /> + <not_has_text text="-M" /> + </assert_command> + <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output> + <output_collection name="matches" type="list" count="2"> + <element name="PopA_01.matches"><assert_contents><has_text text="generated on " /></assert_contents></element> + <element name="PopA_02.matches"><assert_contents><has_text text="generated on " /></assert_contents></element> + </output_collection> + </test> <!-- test w non default parameters and popmap--> <test> <param name="input_cat"> <collection type="list"> - <element name="catalog.alleles.tsv" ftype="tabular" value="cstacks/catalog.alleles.tsv" /> - <element name="catalog.snps.tsv" ftype="tabular" value="cstacks/catalog.snps.tsv" /> - <element name="catalog.tags.tsv" ftype="tabular" value="cstacks/catalog.tags.tsv" /> + <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" /> + <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" /> + <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" /> </collection> </param> - <param name="input_tags"> + <param name="input_stacks"> <collection type="list"> - <element name="PopA_01.alleles.tsv" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" /> - <!-- <element name="PopA_01.matches.tsv" ftype="tabular" value="ustacks/PopA_01.matches.tsv" />--> - <element name="PopA_01.snps.tsv" ftype="tabular" value="ustacks/PopA_01.snps.tsv" /> - <element name="PopA_01.tags.tsv" ftype="tabular" value="ustacks/PopA_01.tags.tsv" /> - <element name="PopA_02.alleles.tsv" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" /> - <!-- <element name="PopA_02.matches.tsv" ftype="tabular" value="ustacks/PopA_02.matches.tsv" />--> - <element name="PopA_02.snps.tsv" ftype="tabular" value="ustacks/PopA_02.snps.tsv" /> - <element name="PopA_02.tags.tsv" ftype="tabular" value="ustacks/PopA_02.tags.tsv" /> + <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" /> + <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" /> + <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" /> + <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" /> + <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" /> + <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" /> </collection> </param> <param name="gapped|use_gapped" value="yes" /> @@ -149,7 +149,7 @@ <has_text text="--disable-gapped" /> <has_text text="-M" /> </assert_command> - <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> + <output name="output_log" ftype="txt"><assert_contents><has_text text="done." /></assert_contents></output> <output_collection name="matches" type="list" count="2"> <element name="PopA_01.matches"><assert_contents><has_text text="generated on " /></assert_contents></element> <element name="PopA_02.matches"><assert_contents><has_text text="generated on " /></assert_contents></element>