Mercurial > repos > matthias > stacks2_tsv2bam
diff stacks_tsv2bam.xml @ 4:60c1c4d7d2c1 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 09:53:30 -0500 |
| parents | 56eb0bc12179 |
| children | 852044374da1 |
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--- a/stacks_tsv2bam.xml Fri Jan 04 03:33:00 2019 -0500 +++ b/stacks_tsv2bam.xml Wed Feb 27 09:53:30 2019 -0500 @@ -1,65 +1,28 @@ -<tool id="stacks2_tsv2bam" name="Stacks2: tsv2bam" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@"> - <description>oriented data by locus</description> +<tool id="stacks2_tsv2bam" name="Stacks2: tsv2bam" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@"> + <description>Sort reads by RAD locus</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> - <expand macro="stdio"/> - <command><![CDATA[ -@CLEAN_EXT@ + <expand macro="version_cmd"/> + <command detect_errors="aggressive"><![CDATA[ +@FASTQ_INPUT_FUNCTIONS@ mkdir stacks_inputs stacks_outputs && -## TODO make token -#set $catalog = "" -#for $input_file in $input_cat - #set $filename = str($input_file.element_identifier) - #if not filename.endswith('.tsv') - #set $filename = $filename + ".tsv" - #end if - #if re.search('catalog\.[a-z]+(\.tsv)?$', $filename) - ln -s '${input_file}' 'stacks_inputs/$filename' && - #if $filename.endswith('.tags.tsv') - #set catalog += " -c 'stacks_inputs/'" - #end if - #end if -#end for - -## TODO make token -#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 $filename.endswith('.tags.tsv') - #set samples += " -s '"+$filename[:-9] + "'" - #end if - #end if -#end for - -## TODO make token -#for $input_file in $input_matches - #set $filename = str($input_file.element_identifier) - #if not filename.endswith('.tsv') - #set $filename = $filename + ".tsv" - #end if - #if re.search('matches.tsv$', $filename) - ln -s '${input_file}' 'stacks_inputs/$filename' && - #end if -#end for +@LINK_STACKS_INPUT@ +@LINK_CAT_INPUT@ +@LINK_MATCHES_INPUT@ ## link fastq files into stacks_inputs/ #set $paired_reads=False -#for $sample in $input_type.samples: +#for $sample in $input_type.fqinputs: #if not $sample: #continue #end if #set $paired_reads=True - #set $read_direction="reverse" - @FASTQ_INPUT@ + #set ($link_cmd, $data_path, $name, $inputype) = $fastq_input_foo($sample, "reverse", ".2") + $link_cmd #end for tsv2bam @@ -67,7 +30,9 @@ #if $popmap -M '$popmap' #else - $samples + #for $sample in $samples + -s '$sample' + #end for #end if #if $paired_reads --pe-reads-dir stacks_inputs @@ -76,19 +41,20 @@ ## tsv2bam writes to stdout and creates a log file ## - make stdout stderr ## - move the additional log file -2>&1 -&& mv stacks_inputs/tsv2bam.log $output_log +2>&1 + +#if $output_log + && mv stacks_inputs/tsv2bam.log $output_log +#end if && mv stacks_inputs/*matches.bam stacks_outputs - ]]></command> <inputs> - <!-- TODO make the inputs macros and use in other tools --> + <expand macro="input_stacks_macro"/> <expand macro="input_cat_macro"/> - <expand macro="input_tags_macro"/> <expand macro="input_matches_macro"/> <!-- TODO add BAM? --> - <expand macro="fastq_input_macro" fastq_optional="true"/> + <expand macro="fastq_input" fastq_optional="true" help="Paired end data or reverse reads. If a paired list is provided only the reverse reads are used in tsv2bam"/> <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" /> <expand macro="in_log"/> </inputs> @@ -103,19 +69,19 @@ <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.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.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="input_matches"> @@ -127,27 +93,27 @@ <param name="add_log" value="yes" /> <output name="output_log" ftype="txt" file="tsv2bam/tsv2bam.log" lines_diff="2"/> <output_collection name="bams" type="list" count="2"> - <element name="PopA_01.matches" file="tsv2bam/PopA_01.matches.bam" ftype="bam" compare="sim_size"/> - <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam" compare="sim_size" /> + <element name="PopA_01.matches" file="tsv2bam/PopA_01.matches.bam" ftype="bam"/> + <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam"/> </output_collection> </test> <!-- test w popmap, w reverse reads as multiple selection --> <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.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.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="input_matches"> @@ -157,32 +123,29 @@ </collection> </param> <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> - <param name="input_type|input_type_selector" value="manual"/> - <param name="input_type|samples" value="demultiplexed/PopA_01.2.fq,demultiplexed/PopA_02.2.fq" ftype="fastqsanger" /> + <param name="input_type|input_type_select" value="single"/> + <param name="input_type|fqinputs" value="demultiplexed/PopA_01.2.fq,demultiplexed/PopA_02.2.fq" ftype="fastqsanger" /> <param name="add_log" value="yes" /> <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> - <output_collection name="bams" type="list" count="2"> - <element name="PopA_01.matches" file="tsv2bam/PopA_01.matches.bam" ftype="bam" compare="sim_size"/> - <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam" compare="sim_size" /> - </output_collection> + <output_collection name="bams" type="list" count="2"/> </test> <!-- test w reverse reads as list --> <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.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.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="input_matches"> @@ -191,8 +154,8 @@ <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv" /> </collection> </param> - <param name="input_type|input_type_selector" value="list"/> - <param name="input_type|samples"> + <param name="input_type|input_type_select" value="paired"/> + <param name="input_type|fqinputs"> <collection type="list"> <element name="PopA_01" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger" /> <element name="PopA_02" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/> @@ -200,28 +163,25 @@ </param> <param name="add_log" value="yes" /> <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> - <output_collection name="bams" type="list" count="2"> - <element name="PopA_01.matches" file="tsv2bam/PopA_01.matches.bam" ftype="bam" compare="sim_size"/> - <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam" compare="sim_size" /> - </output_collection> + <output_collection name="bams" type="list" count="2"/> </test> - <!-- test w paired reads as paired data set list --> + <!-- test w paired reads as paired dataset list --> <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.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.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="input_matches"> @@ -230,8 +190,8 @@ <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv" /> </collection> </param> - <param name="input_type|input_type_selector" value="list"/> - <param name="input_type|samples"> + <param name="input_type|input_type_select" value="paired"/> + <param name="input_type|fqinputs"> <collection type="list:paired"> <element name="PopA_01"> <collection type="paired"> @@ -249,10 +209,7 @@ </param> <param name="add_log" value="yes" /> <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output> - <output_collection name="bams" type="list" count="2"> - <element name="PopA_01.matches" file="tsv2bam/PopA_01.matches.bam" ftype="bam" compare="sim_size"/> - <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam" compare="sim_size" /> - </output_collection> + <output_collection name="bams" type="list" count="2"/> </test> </tests>