| Previous changeset 5:e30352e889fe (2024-10-04) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 |
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modified:
fastq_manipulation.xml macros.xml |
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| diff -r e30352e889fe -r e06d41f3ed3e fastq_manipulation.xml --- a/fastq_manipulation.xml Fri Oct 04 10:34:44 2024 +0000 +++ b/fastq_manipulation.xml Sun Nov 23 17:50:28 2025 +0000 |
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| b'@@ -20,13 +20,8 @@\n #import binascii\n import binascii\n import re\n-import six\n \n-if six.PY2:\n- from string import maketrans\n-else:\n- maketrans = str.maketrans\n-\n+maketrans = str.maketrans\n \n ##does read match\n def match_read(fastq_read):\n@@ -253,162 +248,346 @@\n <!-- match all and do nothing -->\n <test>\n <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />\n- <param name="match_type_selector" value="identifier" />\n- <param name="match_selector" value="regex" />\n- <param name="match_by" value=".*" />\n- <param name="manipulation_type_selector" value="identifier" />\n- <param name="manipulation_selector" value="translate" />\n- <param name="from" value="" />\n- <param name="to" value="" />\n+ <repeat name="match_blocks">\n+ <conditional name="match_type">\n+ <param name="match_type_selector" value="identifier" />\n+ <conditional name="match">\n+ <param name="match_selector" value="regex" />\n+ <param name="match_by" value=".*" />\n+ </conditional>\n+ </conditional>\n+ </repeat>\n+ <repeat name="manipulate_blocks">\n+ <conditional name="manipulation_type">\n+ <param name="manipulation_type_selector" value="identifier" />\n+ <conditional name="manipulation">\n+ <param name="manipulation_selector" value="translate" />\n+ <param name="from" value="" />\n+ <param name="to" value="" />\n+ </conditional>\n+ </conditional>\n+ </repeat>\n <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />\n </test>\n <!-- match None and do nothing -->\n <test>\n <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />\n- <param name="match_type_selector" value="identifier" />\n- <param name="match_selector" value="regex" />\n- <param name="match_by" value="STRINGDOESNOTEXIST" />\n- <param name="manipulation_type_selector" value="identifier" />\n- <param name="manipulation_selector" value="translate" />\n- <param name="from" value="" />\n- <param name="to" value="" />\n+ <repeat name="match_blocks">\n+ <conditional name="match_type">\n+ <param name="match_type_selector" value="identifier" />\n+ <conditional name="match">\n+ <param name="match_selector" value="regex" />\n+ <param name="match_by" value="STRINGDOESNOTEXIST" />\n+ </conditional>\n+ </conditional>\n+ </repeat>\n+ <repeat name="manipulate_blocks">\n+ <conditional name="manipulation_type">\n+ <param name="manipulation_type_selector" value="identifier" />\n+ <conditional name="manipulation">\n+ <param name="manipulation_selector" value="translate" />\n+ <param name="from" value="" />\n+ <param name="to" value="" />\n+ </conditional>\n+ </conditional>\n+ </repeat>\n <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />\n </test>\n <!-- match all and remove -->\n <test>\n <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />\n- <param name="match_type_selector" value="identifier" />\n- <param name="match_selector" value="regex" />\n- <param name="match_by" v'..b'+ <conditional name="match_type">\n+ <param name="match_type_selector" value="identifier" />\n+ <conditional name="match">\n+ <param name="match_selector" value="regex" />\n+ <param name="match_by" value=".*" />\n+ </conditional>\n+ </conditional>\n+ </repeat>\n+ <repeat name="manipulate_blocks">\n+ <conditional name="manipulation_type">\n+ <param name="manipulation_type_selector" value="sequence" />\n+ <conditional name="manipulation">\n+ <param name="manipulation_selector" value="rna_to_dna" />\n+ </conditional>\n+ </conditional>\n+ </repeat>\n <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />\n </test>\n <!-- match all and RNA to DNA (gz compressed) -->\n <test>\n <param name="input_file" value="sanger_full_range_as_rna.fastqsanger.gz" ftype="fastqsanger.gz" />\n- <param name="match_type_selector" value="identifier" />\n- <param name="match_selector" value="regex" />\n- <param name="match_by" value=".*" />\n- <param name="manipulation_type_selector" value="sequence" />\n- <param name="manipulation_selector" value="rna_to_dna" />\n+ <repeat name="match_blocks">\n+ <conditional name="match_type">\n+ <param name="match_type_selector" value="identifier" />\n+ <conditional name="match">\n+ <param name="match_selector" value="regex" />\n+ <param name="match_by" value=".*" />\n+ </conditional>\n+ </conditional>\n+ </repeat>\n+ <repeat name="manipulate_blocks">\n+ <conditional name="manipulation_type">\n+ <param name="manipulation_type_selector" value="sequence" />\n+ <conditional name="manipulation">\n+ <param name="manipulation_selector" value="rna_to_dna" />\n+ </conditional>\n+ </conditional>\n+ </repeat>\n <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger.gz" decompress="true" />\n </test>\n <!-- match all and RNA to DNA (bz2 compressed) -->\n <test>\n <param name="input_file" value="sanger_full_range_as_rna.fastqsanger.bz2" ftype="fastqsanger.bz2" />\n- <param name="match_type_selector" value="identifier" />\n- <param name="match_selector" value="regex" />\n- <param name="match_by" value=".*" />\n- <param name="manipulation_type_selector" value="sequence" />\n- <param name="manipulation_selector" value="rna_to_dna" />\n+ <repeat name="match_blocks">\n+ <conditional name="match_type">\n+ <param name="match_type_selector" value="identifier" />\n+ <conditional name="match">\n+ <param name="match_selector" value="regex" />\n+ <param name="match_by" value=".*" />\n+ </conditional>\n+ </conditional>\n+ </repeat>\n+ <repeat name="manipulate_blocks">\n+ <conditional name="manipulation_type">\n+ <param name="manipulation_type_selector" value="sequence" />\n+ <conditional name="manipulation">\n+ <param name="manipulation_selector" value="rna_to_dna" />\n+ </conditional>\n+ </conditional>\n+ </repeat>\n <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />\n </test>\n </tests>\n' |
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| diff -r e30352e889fe -r e06d41f3ed3e macros.xml --- a/macros.xml Fri Oct 04 10:34:44 2024 +0000 +++ b/macros.xml Sun Nov 23 17:50:28 2025 +0000 |
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| @@ -1,11 +1,11 @@ <macros> - <token name="@TOOL_VERSION@">1.1.5</token> - <token name="@VERSION_SUFFIX@">2</token> - <token name="@PROFILE@">23.1</token> + <token name="@TOOL_VERSION@">1.2</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">24.2</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">galaxy_sequence_utils</requirement> <yield/> </requirements> - </xml>> + </xml> </macros> |