| Previous changeset 7:2505774ded94 (2017-04-07) Next changeset 9:2b1dd7ab69f7 (2017-05-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e |
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modified:
macros.xml stacks_denovomap.xml |
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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 |
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| diff -r 2505774ded94 -r 39d2b6c1c030 macros.xml --- a/macros.xml Fri Apr 07 11:47:48 2017 -0400 +++ b/macros.xml Thu Apr 27 04:17:51 2017 -0400 |
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| @@ -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) |
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| diff -r 2505774ded94 -r 39d2b6c1c030 stacks_denovomap.xml --- a/stacks_denovomap.xml Fri Apr 07 11:47:48 2017 -0400 +++ b/stacks_denovomap.xml Thu Apr 27 04:17:51 2017 -0400 |
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| b'@@ -6,54 +6,47 @@\n <expand macro="requirements"/>\n <expand macro="stdio"/>\n <command><![CDATA[\n- #from os.path import splitext\n- #import re\n \n- #if str( $options_usage.rad_analysis_type ) == "genetic":\n- #for $input_parent in $options_usage.parent_sequences:\n+ @CLEAN_EXT@\n \n- #if $input_parent.is_of_type(\'fastqsanger\'):\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 + ".fq"\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 + ".fa"\n+ #if str( $options_usage.rad_analysis_type ) == "genetic"\n+ #for $input_parent in $options_usage.parent_sequences\n+ #if $input_parent.is_of_type(\'fastqsanger\')\n+ #set $data_path = $clean_ext($input_parent.element_identifier) + ".fq"\n+ #else if $input_parent.is_of_type(\'fastqsanger.gz\')\n+ #set $data_path = $clean_ext($input_parent.element_identifier) + ".fq.gz"\n+ #else\n+ #set $data_path = $clean_ext($input_parent.element_identifier) + ".fa"\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_sequences:\n- #if $input_progeny:\n- #if $input_progeny.is_of_type(\'fastqsanger\'):\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 + ".fq"\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 + ".fa"\n+ #for $input_progeny in $options_usage.progeny_sequences\n+ #if $input_progeny\n+ #if $input_progeny.is_of_type(\'fastqsanger\')\n+ #set $data_path = $clean_ext($input_progeny.element_identifier) + ".fq"\n+ #else if $input_progeny.is_of_type(\'fastqsanger.gz\')\n+ #set $data_path = $clean_ext($input_progeny.element_identifier) + ".fq.gz"\n+ #else\n+ #set $data_path = $clean_ext($input_progeny.element_identifier) + ".fa"\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(\'fastqsanger\'):\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 + ".fq"\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 + ".fa"\n+ #if $input_indiv.is_of_type(\'fastqsanger\')\n+ #set $data_path = $clean_ext($input_indiv.element_identifier) + ".fq"\n+ #else if $input_indiv.is_of_type(\'fastqsanger.gz\')\n+ #set $data_path = $clean_ext($input_indiv.element_identifier) + ".fq.gz"\n+ '..b' <has_text text="Stacks Statistics" />\n+ </assert_contents>\n+ </output>\n \n <!-- catalog -->\n <output name="catalogtags">\n@@ -392,6 +401,11 @@\n <has_text text="denovo_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@@ -467,6 +481,89 @@\n </element>\n </output_collection>\n </test>\n+ <test>\n+ <param name="options_usage|rad_analysis_type" value="genetic"/>\n+ <param name="options_usage|parent_sequences" value="demultiplexed/PopA_01.1.fq.gzip" ftype="fastqsanger.gz" />\n+ <output name="output_log">\n+ <assert_contents>\n+ <has_text text="denovo_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+ <assert_contents>\n+ <has_text text="catalog generated on" />\n+ </assert_contents>\n+ </output>\n+ <output name="catalogsnps">\n+ <assert_contents>\n+ <has_text text="catalog generated on" />\n+ </assert_contents>\n+ </output>\n+ <output name="catalogalleles">\n+ <assert_contents>\n+ <has_text text="catalog generated on" />\n+ </assert_contents>\n+ </output>\n+\n+ <!-- genotypes -->\n+ <output name="out_generic_haplo">\n+ <assert_contents>\n+ <has_text text="Catalog ID" />\n+ </assert_contents>\n+ </output>\n+ <output name="out_sql_markers">\n+ <assert_contents>\n+ <has_text text="Total Genotypes" />\n+ </assert_contents>\n+ </output>\n+ <output name="out_joinmap">\n+ <assert_contents>\n+ <has_text text="batch_1.genotypes_" />\n+ </assert_contents>\n+ </output>\n+ <output name="out_sql_genotypes">\n+ <assert_contents>\n+ <has_text text="SQL ID" />\n+ </assert_contents>\n+ </output>\n+\n+ <!-- samples -->\n+ <output_collection name="tags">\n+ <element name="PopA_01.tags">\n+ <assert_contents>\n+ <has_text text="generated on " />\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ <output_collection name="snps">\n+ <element name="PopA_01.snps">\n+ <assert_contents>\n+ <has_text text="generated on " />\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ <output_collection name="alleles">\n+ <element name="PopA_01.alleles">\n+ <assert_contents>\n+ <has_text text="generated on " />\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ <output_collection name="matches">\n+ <element name="PopA_01.matches">\n+ <assert_contents>\n+ <has_text text="generated on " />\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ </test>\n </tests>\n \n <help>\n' |
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| diff -r 2505774ded94 -r 39d2b6c1c030 test-data/demultiplexed/PopA_01.1.fq.gzip |
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| Binary file test-data/demultiplexed/PopA_01.1.fq.gzip has changed |
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| diff -r 2505774ded94 -r 39d2b6c1c030 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 04:17:51 2017 -0400 |
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| @@ -0,0 +1,1 @@ +PopA_01 myPopA |
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| diff -r 2505774ded94 -r 39d2b6c1c030 test-data/procrad/R1.fq.gzip |
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| Binary file test-data/procrad/R1.fq.gzip has changed |
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| diff -r 2505774ded94 -r 39d2b6c1c030 test-data/ustacks/ustacks.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ustacks/ustacks.out Thu Apr 27 04:17:51 2017 -0400 |
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| @@ -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. |