Mercurial > repos > matthias > stacks2_cstacks
changeset 3:61afc5a3cd8e draft
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 | 8427e904f352 |
| children | 924e7889aa05 |
| files | macros.xml stacks_cstacks.xml todo.txt |
| diffstat | 3 files changed, 26 insertions(+), 13 deletions(-) [+] |
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--- a/macros.xml Tue Dec 18 12:52:48 2018 -0500 +++ b/macros.xml Fri Jan 04 03:31:18 2019 -0500 @@ -128,6 +128,20 @@ </data> </xml> + <!-- inputs from previous pipeline steps --> + <xml name="input_cat_macro"> + <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" /> + </xml> + <xml name="input_tags_macro"> + <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" /> + </xml> + <xml name="input_matches_macro"> + <param name="input_matches" format="tabular,txt" type="data_collection" collection_type="list" label="Matches to the catalog" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or sstacks" /> + </xml> + <xml name="input_aln_macro"> + <param name="input_aln" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P" /> + </xml> + <!-- fastq input --> <xml name="fastq_input_macro" token_fastq_optional="false"> @@ -241,9 +255,9 @@ </xml> <!-- ustacks outputs collection containing SAMPLE.tags.tsv, SAMPLE.snps.tsv, SAMPLE.alleles.tsv (SAMPLE!=catalog) --> - <!-- TODO tags, snps, and alleles could go to sub collections --> + <!-- TODO tags, snps, and alleles could go to sub collections; same for other tools --> <xml name="ustacks_outputs_macro" token_tooladd=""> - <collection name="tabs" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Stacks"> + <collection name="tabs" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Loci per sample"> <discover_datasets pattern="(?P<name>(?!catalog).+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" /> <discover_datasets pattern="(?P<name>(?!catalog).+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" /> <discover_datasets pattern="(?P<name>(?!catalog).+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" /> @@ -251,7 +265,7 @@ </xml> <!-- cstacks outputs collection containing catalog.tags.tsv, catalog.snps.tsv, catalog.alleles.tsv --> <xml name="cstacks_outputs_macro" token_tooladd=""> - <collection name="catalog" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Catalog"> + <collection name="catalog" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Catalog of loci"> <discover_datasets pattern="(?P<name>catalog\.(tags|snps|alleles))\.tsv$" ext="tabular" directory="stacks_outputs" /> </collection> </xml> @@ -263,13 +277,13 @@ </xml> <!-- tsv2bam outputs collection containing SAMPLE.matches.bam --> <xml name="tsv2bam_outputs_macro" token_tooladd=""> - <collection name="bams" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Stacks"> + <collection name="bams" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Loci"> <discover_datasets pattern="(?P<name>.+\.matches)\.bam$" ext="bam" directory="stacks_outputs" /> </collection> </xml> <!-- gstacks outputs collection containing catalog.calls.vcf and catalog.fa.gz --> <xml name="gstacks_outputs_macro" token_tooladd=""> - <collection name="gstacks_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string}"> + <collection name="gstacks_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Assembled contigs and variant sites"> <discover_datasets pattern="(?P<name>catalog\.calls\.vcf)$" ext="vcf" directory="stacks_outputs" /> <discover_datasets pattern="(?P<name>catalog\.fa\.gz)$" ext="fasta.gz" directory="stacks_outputs" /> </collection>
--- a/stacks_cstacks.xml Tue Dec 18 12:52:48 2018 -0500 +++ b/stacks_cstacks.xml Fri Jan 04 03:31:18 2019 -0500 @@ -19,7 +19,7 @@ ## - create -s sample1prefix -s sample2prefix .. #set $samples = "" -#for $input_file in $input_col +#for $input_file in $input_cat #set $filename = str($input_file.element_identifier) #if not filename.endswith('.tsv') #set $filename = $filename + ".tsv" @@ -66,7 +66,7 @@ ]]></command> <inputs> - <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)" /> + <expand macro="input_cat_macro"/> <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" /> @@ -87,7 +87,7 @@ <!-- TODO add test w popmap --> <!-- test w default options --> <test> - <param name="input_col"> + <param name="input_cat"> <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" /> @@ -107,7 +107,7 @@ </test> <!-- test w non default options (wo gapped, because tested already in ustacks) --> <test> - <param name="input_col"> + <param name="input_cat"> <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" /> @@ -140,13 +140,13 @@ **What it does** -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. +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. -------- **Input files** -Output from denovo_map, refmap, ustacks or pstacks +Output from denovo_map, refmap, or ustacks **Output files**