| Previous changeset 11:8665bcc8b847 (2018-03-05) Next changeset 13:f5fdf41c08b8 (2018-06-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488 |
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modified:
cutadapt.xml macros.xml |
| b |
| diff -r 8665bcc8b847 -r 78e1cf88d133 cutadapt.xml --- a/cutadapt.xml Mon Mar 05 11:02:48 2018 -0500 +++ b/cutadapt.xml Thu May 24 18:24:08 2018 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="cutadapt" name="Cutadapt" version="1.16">\n+<tool id="cutadapt" name="Cutadapt" version="1.16.1" profile="17.09">\n <description>Remove adapter sequences from Fastq/Fasta</description>\n <macros>\n <import>macros.xml</import>\n@@ -13,107 +13,62 @@\n \n ## Link in the input and output files, so Cutadapt can tell their type\n \n- #set compressed="False"\n+ #import re\n #set format = "fastq"\n-\n- #if str($library.type) == \'paired\':\n+ #set read1 = "input_f"\n+ #set read2 = "input_r"\n+ #set paired = False\n+ #set library_type = str($library.type)\n+ #if $library_type == \'paired\':\n+ #set paired = True\n+ #set read1 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_1.element_identifier))\n+ #set read2 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_2.element_identifier))\n+ #set input_1 = $library.input_1\n+ #set input_2 = $library.input_2\n+ #else if $library_type == \'paired_collection\'\n+ #set paired = True\n+ #set input_1 = $library.input_1.forward\n+ #set input_2 = $library.input_1.reverse\n+ #set read1 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_1.name))\n+ #else\n+ #set input_1 = $library.input_1\n+ #set read1 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_1.element_identifier))\n+ #end if\n \n- #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):\n- #set read1 = "input_f.fastq.gz"\n- #set compressed = "GZ"\n- #set out1 = "out1.gz"\n- #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n- #set read1 = "input_f.fastq.bz2"\n- #set compressed = "BZ2"\n- #set out1 = "out1.bz2"\n- #else if $library.input_1.is_of_type(\'fasta\'):\n+ #if $input_1.is_of_type("fastq.gz", "fastqsanger.gz"):\n+ #set read1 = $read1 + ".fq.gz"\n+ #set out1 = "out1.gz"\n+ #else if $input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #set read1 = $read1 + ".fq.bz2"\n+ #set out1 = "out1.bz2"\n+ #else if $input_1.is_of_type(\'fasta\'):\n+ #set format = "fasta"\n+ #set read1 = $read1 + ".fa"\n+ #set out1 = "out1.fa"\n+ #else:\n+ #set read1 = $read1 + ".fq"\n+ #set out1 = "out1.fq"\n+ #end if\n+ ln -f -s \'${input_1}\' \'$read1\' &&\n+\n+ #if $paired:\n+ #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"):\n+ #set read2 = $read2 + ".fq.gz"\n+ #set out2 = "out2.gz"\n+ #else if $input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #set read2 = $read2 + ".fq.bz2"\n+ #set out2 = "out2.bz2"\n+ #else if $input_2.is_of_type(\'fasta\'):\n #set format = "fasta"\n- #set read1 = "input_f.fasta"\n- #set out1 = "out1.fa"\n+ #set read2 = $read2 + ".fa"\n+ #set out2 = "out2.fa"\n #else:\n- #set read1 = "input_f.fastq"\n- #set out1 = "out1.fq"\n- #end if\n- ln -f -s \'${library.input_1}\' ${read1} &&\n-\n- #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):\n- #set read2 = "input_r.fastq.gz"\n- #set compressed = "GZ"\n- #set out2 = "out2.gz"\n- #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n- #set read2 = "input_r.fastq.bz2"\n- #set compressed = "BZ2"\n- #set out2 = "out2.bz2"\n- #else if $library.input_2.is_of_type(\'fasta\'):\n- #set read2 = "input_r.fasta"\n- #set out2 = "out2.fa"\n- #set format = "fasta"\n- #else:\n- #set read2 = "input_r.fastq"\n+ #set read2 = $read2 + ".fq"\n #set out2'..b'ource_list2" value="user"/>\n <param name="adapter2" value="AGATCGGAAGAGC"/>\n- <output name="out1" decompress="True" file="cutadapt_out1.fq.gz"/>\n- <output name="out2" decompress="True" file="cutadapt_out2.fq.gz"/>\n+ <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>\n+ <output name="out2" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz"/>\n+ </test>\n+ <!-- Ensure paired collection works -->\n+ <test>\n+ <param name="type" value="paired_collection" />\n+ <param name="input_1">\n+ <collection type="paired">\n+ <element name="forward" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />\n+ <element name="reverse" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />\n+ </collection>\n+ </param>\n+ <param name="adapter_source_list" value="user"/>\n+ <param name="adapter" value="AGATCGGAAGAGC"/>\n+ <param name="adapter_source_list2" value="user"/>\n+ <param name="adapter2" value="AGATCGGAAGAGC"/>\n+ <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>\n+ <output name="out2" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz"/>\n </test>\n <!-- Ensure built-in adapters work -->\n <test>\n@@ -354,7 +332,7 @@\n <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />\n <param name="adapter_source_list" value="builtin"/>\n <param name="adapter" value="TGTAGGCC"/>\n- <output name="out1" file="cutadapt_builtin.out"/>\n+ <output name="out1" file="cutadapt_builtin.out" ftype="fastq"/>\n </test>\n <!-- Ensure discard file output works -->\n <test>\n@@ -365,7 +343,7 @@\n <param name="discard" value="True"/>\n <param name="read_modification" value="none"/>\n <param name="output_type" value="default"/>\n- <output name="out1" file="cutadapt_discard.out"/>\n+ <output name="out1" file="cutadapt_discard.out" ftype="fastq"/>\n </test>\n <!-- Ensure rest file output works -->\n <test>\n@@ -376,8 +354,8 @@\n <param name="read_modification" value="none"/>\n <param name="output_type" value="additional"/>\n <param name="rest_file" value="True"/>\n- <output name="out1" file="cutadapt_rest.out"/>\n- <output name="rest_output" file="cutadapt_rest2.out"/>\n+ <output name="out1" file="cutadapt_rest.out" ftype="fasta"/>\n+ <output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/>\n </test>\n <!-- Ensure nextseq-trim option works -->\n <test>\n@@ -387,7 +365,7 @@\n <param name="adapter" value="AGATCGGAAGAGC"/>\n <param name="read_modification" value="modify"/>\n <param name="nextseq_trim" value="20" />\n- <output name="out1" decompress="True" file="cutadapt_nextseq_out.fq.gz"/>\n+ <output name="out1" decompress="True" file="cutadapt_nextseq_out.fq.gz" ftype="fastq.gz"/>\n </test>\n <!-- Ensure Report and Info file output work -->\n <test>\n@@ -397,13 +375,13 @@\n <param name="adapter" value="AGATCGGAAGAGC"/>\n <param name="report" value="True" />\n <param name="info_file" value="True" />\n- <output name="out1" value="cutadapt_small.out"/>\n+ <output name="out1" value="cutadapt_small.out" ftype="fastq"/>\n <output name="report">\n <assert_contents>\n <has_text text="Summary"/>\n </assert_contents>\n </output>\n- <output name="info_file" value="cutadapt_info_out.txt"/>\n+ <output name="info_file" value="cutadapt_info_out.txt" ftype="txt"/>\n </test>\n </tests>\n \n' |
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| diff -r 8665bcc8b847 -r 78e1cf88d133 macros.xml --- a/macros.xml Mon Mar 05 11:02:48 2018 -0500 +++ b/macros.xml Thu May 24 18:24:08 2018 -0400 |
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| @@ -261,4 +261,43 @@ </xml> + <xml name="inherit_format_1"> + <actions> + <conditional name="library.type"> + <when value="single"> + <action type="format"> + <option type="from_param" name="library.input_1" param_attribute="ext" /> + </action> + </when> + <when value="paired"> + <action type="format"> + <option type="from_param" name="library.input_1" param_attribute="ext" /> + </action> + </when> + <when value="paired_collection"> + <action type="format"> + <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> + </action> + </when> + </conditional> + </actions> + </xml> + + <xml name="inherit_format_2"> + <actions> + <conditional name="library.type"> + <when value="paired"> + <action type="format"> + <option type="from_param" name="library.input_2" param_attribute="ext" /> + </action> + </when> + <when value="paired_collection"> + <action type="format"> + <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> + </action> + </when> + </conditional> + </actions> + </xml> + </macros> \ No newline at end of file |