| Previous changeset 22:093678460093 (2020-07-04) Next changeset 24:288f97432497 (2021-06-02) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818" |
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modified:
cutadapt.xml macros.xml |
| b |
| diff -r 093678460093 -r c4b82dce8335 cutadapt.xml --- a/cutadapt.xml Sat Jul 04 06:52:59 2020 -0400 +++ b/cutadapt.xml Fri Apr 30 10:13:37 2021 +0000 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="cutadapt" name="Cutadapt" version="1.16.8" profile="17.09">\n+<tool id="cutadapt" name="Cutadapt" version="1.16.9" profile="17.09">\n <description>Remove adapter sequences from Fastq/Fasta</description>\n <macros>\n <import>macros.xml</import>\n@@ -93,8 +93,13 @@\n #else:\n @read1_options@\n @read2_options@\n- --output=\'$out1\'\n- --paired-output=\'$out2\'\n+ #if $library.type == "paired"\n+ --output=\'$out1\'\n+ --paired-output=\'$out2\'\n+ #else\n+ --output=\'$out_pairs.forward\'\n+ --paired-output=\'$out_pairs.reverse\'\n+ #end if\n #end if\n \n --error-rate=$adapter_options.error_rate\n@@ -240,14 +245,18 @@\n \n <outputs>\n <data name="out1" format="fastqsanger" metadata_source="input_1" from_work_dir="out1*" label="${tool.name} on ${on_string}: Read 1 Output">\n- <filter>(output_options[\'multiple_output\'] is False)</filter>\n+ <filter>(output_options[\'multiple_output\'] is False and library[\'type\'] != \'paired_collection\')</filter>\n <expand macro="inherit_format_1" />\n </data>\n <data name="out2" format="fastqsanger" metadata_source="input_2" from_work_dir="out2*" label="${tool.name} on ${on_string}: Read 2 Output" >\n- <filter>(library[\'type\'] == \'paired\' or library[\'type\'] == \'paired_collection\')</filter>\n+ <filter>(output_options[\'multiple_output\'] is False and library[\'type\'] == \'paired\')</filter>\n <expand macro="inherit_format_2" />\n </data>\n \n+ <collection name="out_pairs" type="paired" format_source="input_1" label="${tool.name} on ${on_string}: Reads">\n+ <filter>(output_options[\'multiple_output\'] is False and library[\'type\'] == \'paired_collection\')</filter>\n+ </collection>\n+\n <data name="report" format="txt" from_work_dir="report.txt" label="${tool.name} on ${on_string}: Report">\n <filter>(output_options[\'report\'] is True)</filter>\n </data>\n@@ -304,7 +313,7 @@\n \n <tests>\n <!-- Ensure fastq works -->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="type" value="single" />\n <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />\n <param name="adapter_source_list" value="user"/>\n@@ -312,7 +321,7 @@\n <output name="out1" file="cutadapt_small.out" ftype="fastq"/>\n </test>\n <!-- Ensure single end fastq.gz works -->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="type" value="single" />\n <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />\n <param name="adapter_source_list" value="user"/>\n@@ -320,7 +329,7 @@\n <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>\n </test>\n <!-- Ensure paired end fastq.gz works -->\n- <test>\n+ <test expect_num_outputs="2">\n <param name="type" value="paired" />\n <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />\n <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />\n@@ -340,7 +349,7 @@\n </assert_command>\n </test>\n <!-- Ensure paired collection works -->\n- <test>\n+ <test expect_num_outputs="3">\n <param name="type" value="paired_collection" />\n <param name="input_1">\n <collection type="paired">\n@@ -352,11 +361,13 @@\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+ <output_collection name="out_pairs" type="paired">\n+ <element name="forwar'..b'"True" file="cutadapt_out2.fq.gz" ftype="fastq.gz" />\n+ </output_collection>\n </test>\n <!-- Ensure built-in adapters work -->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="type" value="single" />\n <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />\n <param name="adapter_source_list" value="builtin"/>\n@@ -364,7 +375,7 @@\n <output name="out1" file="cutadapt_builtin.out" ftype="fastq"/>\n </test>\n <!-- Ensure discard file output works -->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />\n <param name="adapter_source_list" value="user"/>\n <param name="adapter" value="TTAGACATATCTCCGTCG"/>\n@@ -380,7 +391,7 @@\n </assert_command>\n </test>\n <!-- Ensure rest file output works -->\n- <test>\n+ <test expect_num_outputs="2">\n <param name="input_1" ftype="fasta" value="cutadapt_rest.fa" />\n <param name="adapter_source_list" value="user"/>\n <param name="adapter" value="AAAGATG"/>\n@@ -392,7 +403,7 @@\n <output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/>\n </test>\n <!-- Ensure nextseq-trim option works -->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="type" value="single" />\n <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />\n <param name="adapter_source_list" value="user"/>\n@@ -402,7 +413,7 @@\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+ <test expect_num_outputs="3">\n <param name="type" value="single" />\n <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />\n <param name="adapter_source_list" value="user"/>\n@@ -419,7 +430,7 @@\n </test>\n \n \n- <test>\n+ <test expect_num_outputs="1">\n <conditional name="library">\n <param name="type" value="single" />\n <param name="input_1" ftype="fastq" value="cutadapt_in_split.fastq" />\n@@ -453,7 +464,7 @@\n </output_collection>\n </test>\n \n- <test>\n+ <test expect_num_outputs="1">\n <conditional name="library">\n <param name="type" value="single" />\n <param name="input_1" ftype="fastq.gz" value="cutadapt_in_split.fastq.gz" />\n@@ -480,7 +491,7 @@\n </test>\n \n <!-- Ensure untrimmed file output works -->\n- <test>\n+ <test expect_num_outputs="2">\n <param name="type" value="single" />\n <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />\n <param name="adapter_source_list" value="user"/>\n@@ -490,7 +501,7 @@\n <output name="untrimmed_output" file="cutadapt_untrimmed.out" ftype="fastq"/>\n </test>\n <!-- Ensure untrimmed gzip file output works -->\n- <test>\n+ <test expect_num_outputs="2">\n <param name="type" value="single" />\n <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />\n <param name="adapter_source_list" value="user"/>\n@@ -506,7 +517,7 @@\n <output name="untrimmed_output" file="cutadapt_untrimmed.out.gz" compare="sim_size" delta="4000" ftype="fastq.gz"/>\n </test>\n <!-- same as 1st test with paired data + filter options (because of discard_untrimmed no comparison is done) -->\n- <test>\n+ <test expect_num_outputs="2">\n <param name="type" value="paired" />\n <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />\n <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />\n' |
| b |
| diff -r 093678460093 -r c4b82dce8335 macros.xml --- a/macros.xml Sat Jul 04 06:52:59 2020 -0400 +++ b/macros.xml Fri Apr 30 10:13:37 2021 +0000 |
| b |
| @@ -338,11 +338,6 @@ <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> @@ -355,11 +350,6 @@ <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> |