| Previous changeset 36:64172f1c1202 (2024-01-04) Next changeset 38:b1c926deaa2d (2024-04-15) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1973d7e076969910f753bf31adc0cdda2fc1530f |
|
modified:
cutadapt.xml macros.xml |
| b |
| diff -r 64172f1c1202 -r 944ae523bacb cutadapt.xml --- a/cutadapt.xml Thu Jan 04 18:44:12 2024 +0000 +++ b/cutadapt.xml Thu Mar 21 10:46:29 2024 +0000 |
| [ |
| b'@@ -39,7 +39,7 @@\n #set read1 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_1.element_identifier))\n #end if\n \n-#if $input_1.is_of_type("fastq"):\n+#if $input_1.is_of_type("fastq", "fastq.gz", "fastq.bz2"):\n #set ext = ".fq"\n #else\n #set ext = ".fa"\n@@ -61,14 +61,15 @@\n ln -f -s \'${input_1}\' \'$read1\' &&\n \n #if $paired:\n- #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"):\n- #set ext2 = ".fq.gz"\n- #else if $input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n- #set ext2 = ".fq.gz"\n- #else if $input_2.is_of_type(\'fasta\'):\n+ #if $input_2.is_of_type("fastq", "fastq.gz", "fastq.bz2"):\n+ #set ext2 = ".fq"\n+ #else\n #set ext2 = ".fa"\n- #else:\n- #set ext2 = ".fq"\n+ #end if\n+ #if $input_2.ext.endswith(".gz"):\n+ #set ext2=ext2+".gz"\n+ #elif $input_2.ext.endswith(".bz2")\n+ #set ext2=ext2+".bz2"\n #end if\n #set read2 = $read2 + $ext2\n #set out2 = "out2" + $ext2\n@@ -319,17 +320,17 @@\n </inputs>\n \n <outputs>\n- <data name="out1" format="fastqsanger" metadata_source="input_1" from_work_dir="out1.*" label="${tool.name} on ${on_string}: Read 1 Output">\n+ <data name="out1" format="fastqsanger" metadata_source="library|input_1" default_identifier_source="library|input_1" from_work_dir="out1.*" label="${tool.name} on ${on_string}: Read 1 Output">\n <filter>library[\'type\'] != \'paired_collection\' and \'multiple_output\' not in output_selector</filter>\n <expand macro="inherit_format_1" />\n </data>\n \n- <data name="out2" format="fastqsanger" metadata_source="input_2" from_work_dir="out2.*" label="${tool.name} on ${on_string}: Read 2 Output" >\n+ <data name="out2" format="fastqsanger" metadata_source="library|input_2" default_identifier_source="library|input_2" from_work_dir="out2.*" label="${tool.name} on ${on_string}: Read 2 Output" >\n <filter>library[\'type\'] == \'paired\' and \'multiple_output\' not in output_selector</filter>\n <expand macro="inherit_format_2" />\n </data>\n \n- <collection name="out_pairs" type="paired" format_source="input_1" label="${tool.name} on ${on_string}: Reads">\n+ <collection name="out_pairs" type="paired" format_source="library|input_1" label="${tool.name} on ${on_string}: Reads">\n <filter>library[\'type\'] == \'paired_collection\' and \'multiple_output\' not in output_selector</filter>\n <data name="forward" from_work_dir="out1.*" />\n <data name="reverse" from_work_dir="out2.*" />\n@@ -338,43 +339,43 @@\n <data name="report" format="txt" from_work_dir="report.txt" label="${tool.name} on ${on_string}: Report">\n <filter>output_selector and \'report\' in output_selector</filter>\n </data>\n- <data name="info_file" format="txt" metadata_source="input_1" label="${tool.name} on ${on_string}: Info File" >\n+ <data name="info_file" format="txt" metadata_source="library|input_1" label="${tool.name} on ${on_string}: Info File" >\n <filter>output_selector and \'info_file\' in output_selector</filter>\n </data>\n \n- <data name="rest_output" format="fastqsanger" metadata_source="input_1" from_work_dir="rest_output*" label="${tool.name} on ${on_string}: Rest of Reads (R1 only)" >\n+ <data name="rest_output" format="fastqsanger" metadata_source="library|input_1" from_work_dir="rest_output*" label="${tool.name} on ${on_string}: Rest of Reads (R1 only)" >\n <filter>output_selector and \'rest_file\' in output_selector</filter>\n <expand macro="inherit_format_1" />\n </data>\n \n- <data name="wild_output" format="txt" metadata_source="input_1" from_work_dir="wild_output*" label="${tool.name} on ${on_string}: Wildcard File" >\n+ <data name="wild_output" format="txt" metadata_source="library|input_1" from_work_dir="wild_output*" label="${tool.name} on ${on_string}: Wildcard File" >\n <filter>output_sel'..b'd_output" format="fastqsanger" metadata_source="input_1" from_work_dir="untrimmed_output*" label="${tool.name} on ${on_string}: Untrimmed Read 1" >\n+ <data name="untrimmed_output" format="fastqsanger" metadata_source="library|input_1" default_identifier_source="library|input_1" from_work_dir="untrimmed_output*" label="${tool.name} on ${on_string}: Untrimmed Read 1" >\n <filter>output_selector and \'untrimmed_file\' in output_selector</filter>\n <expand macro="inherit_format_1" />\n </data>\n- <data name="untrimmed_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="untrimmed_paired_output*" label="${tool.name} on ${on_string}: Untrimmed Read 2" >\n+ <data name="untrimmed_paired_output" format="fastqsanger" metadata_source="library|input_2" default_identifier_source="library|input_2" from_work_dir="untrimmed_paired_output*" label="${tool.name} on ${on_string}: Untrimmed Read 2" >\n <filter>library[\'type\'] == \'paired\' or library[\'type\'] == \'paired_collection\'</filter>\n <filter>output_selector and \'untrimmed_file\' in output_selector </filter>\n <expand macro="inherit_format_2" />\n </data>\n \n- <data name="too_short_output" format="fastqsanger" metadata_source="input_1" from_work_dir="too_short_output*" label="${tool.name} on ${on_string}: Too Short Read 1" >\n+ <data name="too_short_output" format="fastqsanger" metadata_source="library|input_1" default_identifier_source="library|input_1" from_work_dir="too_short_output*" label="${tool.name} on ${on_string}: Too Short Read 1" >\n <filter>output_selector and \'too_short_file\' in output_selector</filter>\n <expand macro="inherit_format_1" />\n </data>\n- <data name="too_short_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_short_paired_output*" label="${tool.name} on ${on_string}: Too Short Read 2" >\n+ <data name="too_short_paired_output" format="fastqsanger" metadata_source="library|input_2" default_identifier_source="library|input_2" from_work_dir="too_short_paired_output*" label="${tool.name} on ${on_string}: Too Short Read 2" >\n <filter>library[\'type\'] == \'paired\' or library[\'type\'] == \'paired_collection\'</filter>\n <filter>output_selector and \'too_short_file\' in output_selector</filter>\n <expand macro="inherit_format_2" />\n </data>\n- <data name="too_long_output" format="fastqsanger" metadata_source="input_1" from_work_dir="too_long_output*" label="${tool.name} on ${on_string}: Too Long Read 1" >\n+ <data name="too_long_output" format="fastqsanger" metadata_source="library|input_1" default_identifier_source="library|input_1" from_work_dir="too_long_output*" label="${tool.name} on ${on_string}: Too Long Read 1" >\n <filter>output_selector and \'too_long_file\' in output_selector</filter>\n <expand macro="inherit_format_1" />\n </data>\n- <data name="too_long_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_long_paired_output*" label="${tool.name} on ${on_string}: Too Long Read 2" >\n+ <data name="too_long_paired_output" format="fastqsanger" metadata_source="library|input_2" default_identifier_source="library|input_2" from_work_dir="too_long_paired_output*" label="${tool.name} on ${on_string}: Too Long Read 2" >\n <filter>library[\'type\'] == \'paired\' or library[\'type\'] == \'paired_collection\'</filter>\n <filter>output_selector and \'too_long_file\' in output_selector</filter>\n <expand macro="inherit_format_2" />\n@@ -1333,9 +1334,9 @@\n </conditional>\n </repeat>\n </section>\n- <assert_stdout>\n+ <assert_stderr>\n <has_text text="Reads are improperly paired"/>\n- </assert_stdout>\n+ </assert_stderr>\n </test>\n </tests>\n \n' |
| b |
| diff -r 64172f1c1202 -r 944ae523bacb macros.xml --- a/macros.xml Thu Jan 04 18:44:12 2024 +0000 +++ b/macros.xml Thu Mar 21 10:46:29 2024 +0000 |
| b |
| @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">4.6</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">4.7</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@FASTQ_TYPES@">fastq.bz2,fastq.gz,fastq,fasta.bz2,fasta.gz,fasta</token> <xml name="edam_ontology"> <edam_topics> |