| Previous changeset 2:ba76bd1eef47 (2016-06-15) Next changeset 4:827c8c6ec4c1 (2016-09-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 |
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modified:
macros.xml stacks_refmap.xml tool_dependencies.xml |
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| diff -r ba76bd1eef47 -r 26ad8a52d9fd macros.xml --- a/macros.xml Wed Jun 15 06:25:14 2016 -0400 +++ b/macros.xml Sat Jun 25 17:29:09 2016 -0400 |
| [ |
| @@ -117,11 +117,11 @@ ln -s batch_1.genotypes_*onemap.tsv batch_1.genotypes.onemap.tsv && ln -s batch_1.genotypes_*.onemap.txt batch_1.genotypes.onemap.txt && ln -s batch_1.genomic_*.tsv batch_1.genomic.tsv && - ln -s batch_1.genotypes_1.rqtl.tsv batch_1.genotypes.rqtl.tsv && - ln -s batch_1.haplotypes_1.tsv batch_1.haplotypes.tsv && + ln -s batch_1.genotypes_*.rqtl.tsv batch_1.genotypes.rqtl.tsv && + ln -s batch_1.haplotypes_*.tsv batch_1.haplotypes.tsv && ln -s batch_1.genotypes_*.loc batch_1.genotypes.loc && - ln -s batch_1.genotypes_1.txt batch_1.genotypes.txt && - ln -s batch_1.genotypes_1.tsv batch_1.genotypes.tsv && + ln -s batch_1.genotypes_*.txt batch_1.genotypes.txt && + ln -s batch_1.genotypes_*[^rqtl].tsv batch_1.genotypes.tsv && cd .. ]]> </token> |
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| diff -r ba76bd1eef47 -r 26ad8a52d9fd stacks_refmap.xml --- a/stacks_refmap.xml Wed Jun 15 06:25:14 2016 -0400 +++ b/stacks_refmap.xml Sat Jun 25 17:29:09 2016 -0400 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="stacks_refmap" name="Stacks: reference map" version="@WRAPPER_VERSION@.0">\n+<tool id="stacks_refmap" name="Stacks: reference map" version="@WRAPPER_VERSION@.1">\n <description>the Stacks pipeline with a reference genome (ref_map.pl)</description>\n <macros>\n <import>macros.xml</import>\n@@ -12,11 +12,11 @@\n #if str( $options_usage.rad_analysis_type ) == "genetic":\n #for $input_parent in $options_usage.parent_alignments:\n #if $input_parent.ext == "sam":\n- #set $data_path = splitext($input_parent.name)[0]\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.name)[0]\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 #end if\n@@ -26,27 +26,29 @@\n \n #for $input_progeny in $options_usage.progeny_alignments:\n \n- #if $input_progeny.ext == "sam":\n- #set $data_path = splitext($input_progeny.name)[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.name)[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.ext == "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 = $data_path + ".bam"\n+ #end if\n+\n+ ln -s "${input_progeny}" "${data_path}" &&\n #end if\n-\n- ln -s "${input_progeny}" "${data_path}" &&\n #end for\n #else:\n #for $input_indiv in $options_usage.individual_sample:\n \n #if $input_indiv.ext == "sam":\n- #set $data_path = splitext($input_indiv.name)[0]\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.name)[0]\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 #end if\n@@ -66,11 +68,11 @@\n #if str( $options_usage.rad_analysis_type ) == "genetic":\n #for $input_parent in $options_usage.parent_alignments:\n #if $input_parent.ext == "sam":\n- #set $data_path = splitext($input_parent.name)[0]\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.name)[0]\n+ #set $data_path = splitext($input_parent.element_identifier)[0]\n #set $'..b'" ext="tabular" directory="stacks_outputs" />\n+ <discover_datasets pattern="(?P<name>.+\\.(genotypes))\\.(loc|txt)$" ext="txt" directory="stacks_outputs" />\n </collection>\n </outputs>\n \n@@ -208,6 +212,94 @@\n <test>\n <param name="options_usage|rad_analysis_type" value="genetic"/>\n <param name="options_usage|parent_alignments" value="refmap/PopA_01.bam" />\n+ <output name="output_log">\n+ <assert_contents>\n+ <has_text text="ref_map.pl completed" />\n+ </assert_contents>\n+ </output>\n+\n+ <!-- catalog -->\n+ <output name="catalogsnps">\n+ <assert_contents>\n+ <has_text text="catalog generated" />\n+ </assert_contents>\n+ </output>\n+ <output name="catalogalleles">\n+ <assert_contents>\n+ <has_text text="catalog generated" />\n+ </assert_contents>\n+ </output>\n+ <output name="catalogtags">\n+ <assert_contents>\n+ <has_text text="catalog generated" />\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+ <output name="out_generic_haplo">\n+ <assert_contents>\n+ <has_text text="Seg Dist" />\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+\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+ <test>\n+ <param name="options_usage|rad_analysis_type" value="genetic"/>\n+ <param name="options_usage|parent_alignments" value="refmap/PopA_01.bam" />\n <param name="options_usage|progeny_alignments" value="refmap/PopA_02.bam" />\n <output name="output_log">\n <assert_contents>\n' |
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| diff -r ba76bd1eef47 -r 26ad8a52d9fd tool_dependencies.xml --- a/tool_dependencies.xml Wed Jun 15 06:25:14 2016 -0400 +++ b/tool_dependencies.xml Sat Jun 25 17:29:09 2016 -0400 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="stacks" version="1.40"> - <repository changeset_revision="95cffefc0dfe" name="package_stacks_1_40" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="51d4ab2c4dcf" name="package_stacks_1_40" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="velvet" version="1.2.10"> <repository changeset_revision="93d32326537b" name="package_velvet_1_2_10" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> |