Mercurial > repos > matthias > stacks2_denovomap
changeset 6:dddd1a6454ce draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 82e7263f3e57a29362d981e36b82b82063f12ac3
| author | matthias |
|---|---|
| date | Tue, 25 Jun 2019 10:59:31 -0400 |
| parents | 3680074758c5 |
| children | |
| files | macros.xml stacks_denovomap.xml test-data/.gentest.sh.swp |
| diffstat | 3 files changed, 29 insertions(+), 42 deletions(-) [+] |
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--- a/macros.xml Thu Jun 20 08:14:41 2019 -0400 +++ b/macros.xml Tue Jun 25 10:59:31 2019 -0400 @@ -107,12 +107,12 @@ <!-- log file handling --> <token name="@TEE_APPEND_LOG@"><![CDATA[ #if $output_log - 2>> $output_log && + 2>> '$output_log' && #end if ]]></token> <token name="@CAT_LOG_TO_STDERR@"><![CDATA[ #if $output_log - cat $output_log 2>&1 + cat '$output_log' 2>&1 #end if ]]></token> <xml name="in_log"> @@ -216,11 +216,15 @@ </expand> </xml> - <!-- fastq input (used in denovomap, tsv2bam, ustacks) --> - <xml name="fastq_input" token_fastq_optional="false" token_help=""> + <!-- fastq input (used in denovomap, tsv2bam, ustacks) + - fastq_optional: makes fastq input optional (true/false) + - se_option: wording for "single end" option (for tsv2bam this is the + reverse reads for the others its the forward reads) + - help: help text --> + <xml name="fastq_input" token_fastq_optional="false" token_se_option="single end or forward reads" token_help=""> <conditional name="input_type"> <param name="input_type_select" type="select" label="Short read data from individuals" help="@HELP@"> - <option value="single" selected="true">single end or forward reads</option> + <option value="single" selected="true">@SE_OPTION@</option> <option value="paired">(paired) dataset list</option> </param> <when value="single">
--- a/stacks_denovomap.xml Thu Jun 20 08:14:41 2019 -0400 +++ b/stacks_denovomap.xml Tue Jun 25 10:59:31 2019 -0400 @@ -9,7 +9,6 @@ @FASTQ_INPUT_FUNCTIONS@ mkdir stacks_inputs stacks_outputs&& - #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, ".%d" ) $link_command @@ -25,7 +24,12 @@ -n $assembly_options.n --var-alpha $model_options.var_alpha --gt-alpha $model_options.gt_alpha -$paired +#if $input_type.input_type_select == "paired" + --paired +#end if +$pe_options.rm_pcr_duplicates +--min-samples-per-pop $popfilter_options.min_samples_per_pop +--min-populations $popfilter_options.min_populations ## the catalog.calls output is a gzip-ed vcf extract it ## to make it usable in Galaxy (with the downside that we @@ -41,10 +45,16 @@ <param name="M" argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual" help="used in ustacks"/> <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between loci when building the catalog" help="used in cstacks; suggested: set to -M"/> </section> - <section name="model_options" title="Variant calling options (for gstacks)" expanded="true"> + <section name="model_options" title="SNP model options" expanded="true"> <expand macro="variant_calling_options_vg" varalpha_default="0.01"/> </section> - <param argument="--paired" type="boolean" checked="false" truevalue="--paired" falsevalue="" label="Use paired-end reads to assemble mini-contigs" help="After assembling RAD loci (in the tsv2bam step)" /> + <section name="pe_options" title="Paired-end options" expanded="true"> + <param argument="--rm-pcr-duplicates" name="rm_pcr_duplicates" type="boolean" checked="false" truevalue="--rm-pcr-duplicates" falsevalue="" label="remove all but one set of read pairs of the same sample that have the same insert length" help="" /> + </section> + <section name="popfilter_options" title="Population filtering options" expanded="true"> + <param argument="--min-samples-per-pop" name="min_samples_per_pop" type="integer" value="0" label="minimum percentage of individuals in a population required to process a locus for that population" help="(for populations; default: 0)"/> + <param argument="--min-populations" name="min_populations" type="integer" value="1" label="minimum number of populations a locus must be present in to process a locus" help="(for populations; default: 1)" /> + </section> <expand macro="in_log"/> </inputs> <outputs> @@ -82,7 +92,6 @@ </collection> </param> <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> - <param name="paired" value="--paired" /> <output_collection name="tabs" count="6"> <element name="PopA_01.tags" file="ustacks/PopA_01.tags.tsv" ftype="tabular" lines_diff="2"/> <element name="PopA_01.snps" file="ustacks/PopA_01.snps.tsv" ftype="tabular" lines_diff="2"/> @@ -146,11 +155,17 @@ <param name="assembly_options|n" value="3" /> <param name="model_options|var_alpha" value="0.1" /> <param name="model_options|gt_alpha" value="0.1" /> + <param name="pe_options|rm_pcr_duplicates" value="--rm-pcr-duplicates" /> + <param name="popfilter_options|min_samples_per_pop" value="1"/> + <param name="popfilter_options|min_populations" value="0" /> <assert_command> <has_text text="-M 3" /> <has_text text="-n 3" /> <has_text text="\-\-var-alpha 0.1" /> <has_text text="\-\-gt-alpha 0.1" /> + <has_text text="\-\-rm-pcr-duplicates" /> + <has_text text="\-\-min-samples-per-pop 1" /> + <has_text text="\-\-min-populations 0" /> </assert_command> <output_collection name="tabs" count="6"/> <output_collection name="catalog" type="list" count="3"/> @@ -164,38 +179,6 @@ <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output> <output ftype="tabular" name="out_sql"><assert_contents><has_text text="#"/></assert_contents></output> </test> - <!-- paired input, deafults (not using reverse reads), testing against the output of the pipeline components (note, this is equal because reverse reads are not used) --> - <test> - <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"> - <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" /> - <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/> - </collection> - </element> - <element name="PopA_02"> - <collection type="paired"> - <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger" /> - <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/> - </collection> - </element> - </collection> - </param> - <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> - <output_collection name="tabs" count="6"/> - <output_collection name="catalog" type="list" count="3"/> - <output_collection name="matches" type="list" count="2"/> - <output_collection name="bams" type="list" count="2"/> - <output_collection name="gstacks_out" type="list" count="2"/> - <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="#"/></assert_contents></output> - <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="#"/></assert_contents></output> - <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="#"/></assert_contents></output> - <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="#"/></assert_contents></output> - <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output> - <output ftype="tabular" name="out_sql"><assert_contents><has_text text="#"/></assert_contents></output> - </test> </tests> <help>