| Previous changeset 7:14396ffcb253 (2017-04-07) Next changeset 9:4ee074ca88fb (2017-05-21) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e |
|
modified:
macros.xml stacks_refmap.xml |
|
added:
test-data/demultiplexed/PopA_01.1.fq.gzip test-data/denovo_map/popmap_cstacks.tsv test-data/procrad/R1.fq.gzip test-data/ustacks/ustacks.out |
| b |
| diff -r 14396ffcb253 -r c209e3f3359b macros.xml --- a/macros.xml Fri Apr 07 11:46:59 2017 -0400 +++ b/macros.xml Thu Apr 27 04:17:01 2017 -0400 |
| [ |
| @@ -2,14 +2,14 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="1.42">stacks</requirement> + <requirement type="package" version="1.46">stacks</requirement> <requirement type="package" version="1.2.10">velvet</requirement> - <container type="docker">quay.io/biocontainers/stacks:1.42--2</container> + <requirement type="package" version="1.1">stacks_summary</requirement> <yield/> </requirements> </xml> - <token name="@WRAPPER_VERSION@">1.42</token> + <token name="@WRAPPER_VERSION@">1.46</token> <xml name="stdio"> <stdio> @@ -90,6 +90,7 @@ <option value="bsaHI">bsaHI</option> <option value="hpaII">hpaII</option> <option value="ncoI">ncoI</option> + <option value="ApaLI">ApaLI</option> </xml> <xml name="cross_types"> @@ -100,6 +101,19 @@ <option value="GEN">GEN (generic, unspecific to any map type)</option> </xml> + <token name="@CLEAN_EXT@"> + <![CDATA[ + #from os.path import splitext + #import re + #def clean_ext($identifier) + #while $identifier.endswith(('.1', '.fa', '.fq', '.fasta', '.fastq', '.gz', '.gzip', '.sam', '.bam')) + #set $identifier = splitext($identifier)[0] + #end while +$identifier#slurp + #end def + ]]> + </token> + <token name="@NORM_GENOTYPES_OUTPUT_LIGHT@"> <![CDATA[ ## We need to do this as the output file names contains the value of an option (min progeny) |
| b |
| diff -r 14396ffcb253 -r c209e3f3359b stacks_refmap.xml --- a/stacks_refmap.xml Fri Apr 07 11:46:59 2017 -0400 +++ b/stacks_refmap.xml Thu Apr 27 04:17:01 2017 -0400 |
| [ |
| b'@@ -6,54 +6,42 @@\n <expand macro="requirements"/>\n <expand macro="stdio"/>\n <command><![CDATA[\n- #from os.path import splitext\n- #import re\n+\n+ @CLEAN_EXT@\n \n- #if str( $options_usage.rad_analysis_type ) == "genetic":\n- #for $input_parent in $options_usage.parent_alignments:\n- #if $input_parent.is_of_type(\'sam\'):\n- #set $data_path = splitext($input_parent.element_identifier)[0]\n- #set $data_path = re.sub(r\'\\.1$\', \'\', $data_path)\n- #set $data_path = $data_path + ".sam"\n- #else:\n- #set $data_path = splitext($input_parent.element_identifier)[0]\n- #set $data_path = re.sub(r\'\\.1$\', \'\', $data_path)\n- #set $data_path = $data_path + ".bam"\n+ #if str( $options_usage.rad_analysis_type ) == "genetic"\n+ #for $input_parent in $options_usage.parent_alignments\n+ #if $input_parent.is_of_type(\'sam\')\n+ #set $data_path = $clean_ext($input_parent.element_identifier) + ".sam"\n+ #else\n+ #set $data_path = $clean_ext($input_parent.element_identifier) + ".bam"\n #end if\n \n- ln -s "${input_parent}" "${data_path}" &&\n+ ln -s \'${input_parent}\' \'${data_path}\' &&\n #end for\n \n- #for $input_progeny in $options_usage.progeny_alignments:\n+ #for $input_progeny in $options_usage.progeny_alignments\n \n- #if $input_progeny:\n- #if $input_progeny.is_of_type(\'sam\'):\n- #set $data_path = splitext($input_progeny.element_identifier)[0]\n- #set $data_path = re.sub(r\'\\.1$\', \'\', $data_path)\n- #set $data_path = $data_path + ".sam"\n- #else:\n- #set $data_path = splitext($input_progeny.element_identifier)[0]\n- #set $data_path = re.sub(r\'\\.1$\', \'\', $data_path)\n- #set $data_path = $data_path + ".bam"\n+ #if $input_progeny\n+ #if $input_progeny.is_of_type(\'sam\')\n+ #set $data_path = $clean_ext($input_progeny.element_identifier) + ".sam"\n+ #else\n+ #set $data_path = $clean_ext($input_progeny.element_identifier) + ".bam"\n #end if\n \n- ln -s "${input_progeny}" "${data_path}" &&\n+ ln -s \'${input_progeny}\' \'${data_path}\' &&\n #end if\n #end for\n- #else:\n- #for $input_indiv in $options_usage.individual_sample:\n+ #else\n+ #for $input_indiv in $options_usage.individual_sample\n \n- #if $input_indiv.is_of_type(\'sam\'):\n- #set $data_path = splitext($input_indiv.element_identifier)[0]\n- #set $data_path = re.sub(r\'\\.1$\', \'\', $data_path)\n- #set $data_path = $data_path + ".sam"\n- #else:\n- #set $data_path = splitext($input_indiv.element_identifier)[0]\n- #set $data_path = re.sub(r\'\\.1$\', \'\', $data_path)\n- #set $data_path = $data_path + ".bam"\n+ #if $input_indiv.is_of_type(\'sam\')\n+ #set $data_path = $clean_ext($input_indiv.element_identifier) + ".sam"\n+ #else\n+ #set $data_path = $clean_ext($input_indiv.element_identifier) + ".bam"\n #end if\n \n- ln -s "${input_indiv}" "${data_path}" &&\n+ ln -s \'${input_indiv}\' \'${data_path}\' &&\n #end for\n #end if\n \n@@ -65,60 +53,48 @@\n \n -T \\${GALAXY_SLOTS:-1}\n \n- #if str( $options_usage.rad_analysis_type ) == "genetic":\n- #for $input_parent in $options_usage.parent_alignments:\n- #if $input_p'..b'r) + ".bam"\n #end if\n \n- -s "${data_path}"\n+ -s \'${data_path}\'\n #end for\n- -O "$options_usage.popmap"\n+ -O \'$options_usage.popmap\'\n #end if\n \n- #if str($m):\n+ #if str($m)\n -m $m\n #end if\n- #if str($P):\n+ #if str($P)\n -P $P\n #end if\n \n@@ -129,22 +105,29 @@\n -S\n \n ## snp_model\n- #if str( $snp_options.select_model.model_type) == "bounded":\n+ #if str( $snp_options.select_model.model_type) == "bounded"\n --bound_low $snp_options.select_model.bound_low\n --bound_high $snp_options.select_model.bound_high\n --alpha $snp_options.select_model.alpha\n- #else if str( $snp_options.select_model.model_type) == "snp":\n+ #else if str( $snp_options.select_model.model_type) == "snp"\n --alpha $snp_options.select_model.alpha\n #end if\n \n -o stacks_outputs\n \n- #if str( $options_usage.rad_analysis_type ) == "genetic":\n+ #if str( $options_usage.rad_analysis_type ) == "genetic"\n @NORM_GENOTYPES_OUTPUT_LIGHT@\n #end if\n \n ## If input is in bam format, stacks will output gzipped files (no option to control this)\n && if ls stacks_outputs/*.gz > /dev/null 2>&1; then gunzip stacks_outputs/*.gz; fi\n+\n+ &&\n+\n+ stacks_summary.py --stacks-prog ref_map.pl --res-dir stacks_outputs --logfile stacks_outputs/ref_map.log --summary stacks_outputs/summary.html\n+ #if str( $options_usage.rad_analysis_type ) == "population":\n+ --pop-map \'$options_usage.popmap\'\n+ #end if\n ]]></command>\n \n <inputs>\n@@ -178,6 +161,8 @@\n <outputs>\n <data format="txt" name="output_log" label="ref_map.log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/ref_map.log" />\n \n+ <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />\n+\n <data format="tabular" name="catalogtags" label="Catalog assembled loci (tags) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.tags.tsv" />\n <data format="tabular" name="catalogsnps" label="Catalog model calls (snps) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.snps.tsv" />\n <data format="tabular" name="catalogalleles" label="Catalog haplotypes (alleles) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.alleles.tsv" />\n@@ -217,6 +202,11 @@\n <has_text text="ref_map.pl completed" />\n </assert_contents>\n </output>\n+ <output name="output_summary">\n+ <assert_contents>\n+ <has_text text="Stacks Statistics" />\n+ </assert_contents>\n+ </output>\n \n <!-- catalog -->\n <output name="catalogsnps">\n@@ -306,6 +296,11 @@\n <has_text text="ref_map.pl completed" />\n </assert_contents>\n </output>\n+ <output name="output_summary">\n+ <assert_contents>\n+ <has_text text="Stacks Statistics" />\n+ </assert_contents>\n+ </output>\n \n <!-- catalog -->\n <output name="catalogsnps">\n@@ -395,6 +390,11 @@\n <has_text text="ref_map.pl completed" />\n </assert_contents>\n </output>\n+ <output name="output_summary">\n+ <assert_contents>\n+ <has_text text="Stacks Statistics" />\n+ </assert_contents>\n+ </output>\n \n <!-- catalog -->\n <output name="catalogtags">\n' |
| b |
| diff -r 14396ffcb253 -r c209e3f3359b test-data/demultiplexed/PopA_01.1.fq.gzip |
| b |
| Binary file test-data/demultiplexed/PopA_01.1.fq.gzip has changed |
| b |
| diff -r 14396ffcb253 -r c209e3f3359b test-data/denovo_map/popmap_cstacks.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/denovo_map/popmap_cstacks.tsv Thu Apr 27 04:17:01 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +PopA_01 myPopA |
| b |
| diff -r 14396ffcb253 -r c209e3f3359b test-data/procrad/R1.fq.gzip |
| b |
| Binary file test-data/procrad/R1.fq.gzip has changed |
| b |
| diff -r 14396ffcb253 -r c209e3f3359b test-data/ustacks/ustacks.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ustacks/ustacks.out Thu Apr 27 04:17:01 2017 -0400 |
| b |
| @@ -0,0 +1,41 @@ +ustacks parameters selected: + Sample ID: 1 + Min depth of coverage to create a stack: 2 + Max distance allowed between stacks: 2 + Max distance allowed to align secondary reads: 4 + Max number of stacks allowed per de novo locus: 3 + Deleveraging algorithm: disabled + Removal algorithm: enabled + Model type: SNP + Alpha significance level for model: 0.05 + Gapped alignments: disabled +Parsing stacks_inputs/PopA_01.fq +Loading RAD-Tags...done +Loaded 66 RAD-Tags. + Inserted 7 elements into the RAD-Tags hash map. + 0 reads contained uncalled nucleotides that were modified. +4 initial stacks were populated; 3 stacks were set aside as secondary reads. +Initial coverage mean: 15.75; Std Dev: 7.46241; Max: 27 +Deleveraging trigger: 23; Removal trigger: 31 +Calculating distance for removing repetitive stacks. + Distance allowed between stacks: 1; searching with a k-mer length of 47 (48 k-mers per read); 1 k-mer hits required. +Removing repetitive stacks. + Removed 0 stacks. + 4 stacks remain for merging. +Post-Repeat Removal, coverage depth Mean: 15.75; Std Dev: 7.46241; Max: 27 +Calculating distance between stacks... + Distance allowed between stacks: 2; searching with a k-mer length of 31 (64 k-mers per read); 2 k-mer hits required. +Merging stacks, maximum allowed distance: 2 nucleotide(s) + 4 stacks merged into 3 loci; deleveraged 0 loci; blacklisted 0 loci. +After merging, coverage depth Mean: 21; Std Dev: 4.24264; Max: 27 +Merging remainder radtags + 3 remainder sequences left to merge. + Distance allowed between stacks: 4; searching with a k-mer length of 17 (78 k-mers per read); 10 k-mer hits required. + Matched 3 remainder reads; unable to match 0 remainder reads. +After remainders merged, coverage depth Mean: 22; Std Dev: 4.32049; Max: 28 +Calling final consensus sequences, invoking SNP-calling model... +Number of utilized reads: 66 +Writing loci, SNPs, and alleles to 'stacks_outputs/'... + Refetching sequencing IDs from stacks_inputs/PopA_01.fq... read 66 sequence IDs. +done. +ustacks is done. |