Mercurial > repos > iuc > stacks_pstacks
diff stacks_pstacks.xml @ 8:f42f9ae6d109 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
author | iuc |
---|---|
date | Thu, 27 Apr 2017 04:17:39 -0400 |
parents | c9413b0ba604 |
children | 67cbd80b83f5 |
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--- a/stacks_pstacks.xml Fri Apr 07 11:47:36 2017 -0400 +++ b/stacks_pstacks.xml Thu Apr 27 04:17:39 2017 -0400 @@ -6,26 +6,22 @@ <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ - #from os.path import splitext - #import re + + @CLEAN_EXT@ mkdir stacks_inputs stacks_outputs && - #if $sample.is_of_type('sam'): - #set $data_path = splitext($sample.element_identifier)[0] - #set $data_path = re.sub(r'\.1$', '', $data_path) - #set $data_path = "stacks_inputs/" + $data_path + ".sam" + #if $sample.is_of_type('sam') + #set $data_path = "stacks_inputs/" + $clean_ext($sample.element_identifier) + ".sam" #set inputype = "sam" - #else: - #set $data_path = splitext($sample.element_identifier)[0] - #set $data_path = re.sub(r'\.1$', '', $data_path) - #set $data_path = "stacks_inputs/" + $data_path + ".bam" + #else + #set $data_path = "stacks_inputs/" + $clean_ext($sample.element_identifier) + ".bam" #set inputype = "bam" #end if - ln -s "${sample}" "${data_path}" + ln -s '${sample}' '${data_path}' && @@ -42,13 +38,17 @@ -m $m + --max_clipped $max_clipped + --min_mapq $min_mapq + $keep_sec_alns + ## snp_model - #if str( $snp_options.select_model.model_type) == "bounded": + #if str( $snp_options.select_model.model_type) == "bounded" --model_type bounded --bound_low $snp_options.select_model.bound_low --bound_high $snp_options.select_model.bound_high --alpha $snp_options.select_model.alpha - #else if str( $snp_options.select_model.model_type) == "snp": + #else if str( $snp_options.select_model.model_type) == "snp" --model_type snp --alpha $snp_options.select_model.alpha #else @@ -58,19 +58,28 @@ -o stacks_outputs - > pstacks.log 2>&1 + 2>&1 | tee pstacks.log ## If input is in bam format, stacks will output gzipped files (no option to control this) && if ls stacks_outputs/*.gz > /dev/null 2>&1; then gunzip stacks_outputs/*.gz; fi + + && + + stacks_summary.py --stacks-prog pstacks --res-dir stacks_outputs --logfile pstacks.log --summary stacks_outputs/summary.html ]]></command> <inputs> - <param name="sample" argument="-f" format="fastqsanger,fasta" type="data" label="Input short reads from an individual" /> + <param name="sample" argument="-f" format="sam,bam" type="data" label="Input short reads from an individual" /> <param name="sample_id" argument="-i" type="integer" value="" label="Give a unique numeric ID to this sample"/> <param name="m" argument="-m" type="integer" value="1" label="Minimum depth of coverage required to create a stack"/> + <param name="max_clipped" argument="--max_clipped" type="float" value="0.15" min="0.0" max="1.0" label="Alignments with more than this fraction of soft-clipped bases are discarded"/> + + <param name="min_mapq" argument="--min_mapq" type="integer" value="10" label="Minimum required mapping quality"/> + + <param name="keep_sec_alns" argument="--keep_sec_alns" type="boolean" checked="false" truevalue="--keep_sec_alns" falsevalue="" label="Keep secondary alignments" /> <!-- SNP Model options --> <section name="snp_options" title="SNP Model Options (pstacks options)" expanded="False"> @@ -80,6 +89,9 @@ <outputs> <data format="txt" name="output_log" label="pstacks.log with ${tool.name} on ${on_string}" from_work_dir="pstacks.log" /> + + <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" /> + <collection name="tabs" type="list" label="Stacks from ${on_string}"> <discover_datasets pattern="(?P<name>.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" /> <discover_datasets pattern="(?P<name>.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" /> @@ -98,6 +110,11 @@ <has_text text="done." /> </assert_contents> </output> + <output name="output_summary"> + <assert_contents> + <has_text text="Stacks Statistics" /> + </assert_contents> + </output> <output_collection name="tabs"> <element name="PopA_01.tags">