| Previous changeset 5:144275714590 (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_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9 |
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modified:
fastq_filter.xml macros.xml |
| b |
| diff -r 144275714590 -r ff7d49ec777f fastq_filter.xml --- a/fastq_filter.xml Fri Oct 04 10:34:25 2024 +0000 +++ b/fastq_filter.xml Sun Nov 23 17:50:05 2025 +0000 |
| b |
| b'@@ -109,12 +109,16 @@\n <param name="max_quality" value="0"/>\n <param name="max_num_deviants" value="0"/>\n <param name="paired_end" value="false"/>\n- <param name="base_offset_type" value="offsets_absolute"/>\n- <param name="left_column_offset" value="0"/>\n- <param name="right_column_offset" value="0"/>\n- <param name="score_operation" value="min"/>\n- <param name="score_comparison" value=">="/>\n- <param name="score" value="0"/>\n+ <repeat name="fastq_filters">\n+ <conditional name="offset_type">\n+ <param name="base_offset_type" value="offsets_absolute"/>\n+ <param name="left_column_offset" value="0"/>\n+ <param name="right_column_offset" value="0"/>\n+ </conditional>\n+ <param name="score_operation" value="min"/>\n+ <param name="score_comparison" value=">="/>\n+ <param name="score" value="0"/>\n+ </repeat>\n <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />\n </test>\n <!-- Do nothing filter compressed -->\n@@ -126,12 +130,16 @@\n <param name="max_quality" value="0"/>\n <param name="max_num_deviants" value="0"/>\n <param name="paired_end" value="false"/>\n- <param name="base_offset_type" value="offsets_absolute"/>\n- <param name="left_column_offset" value="0"/>\n- <param name="right_column_offset" value="0"/>\n- <param name="score_operation" value="min"/>\n- <param name="score_comparison" value=">="/>\n- <param name="score" value="0"/>\n+ <repeat name="fastq_filters">\n+ <conditional name="offset_type">\n+ <param name="base_offset_type" value="offsets_absolute"/>\n+ <param name="left_column_offset" value="0"/>\n+ <param name="right_column_offset" value="0"/>\n+ </conditional>\n+ <param name="score_operation" value="min"/>\n+ <param name="score_comparison" value=">="/>\n+ <param name="score" value="0"/>\n+ </repeat>\n <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger.gz" ftype="fastqsanger.gz" decompress="true"/>\n </test>\n <!-- crippled input types prevent this test <test>\n@@ -159,12 +167,16 @@\n <param name="max_quality" value="0"/>\n <param name="max_num_deviants" value="0"/>\n <param name="paired_end" value="false"/>\n- <param name="base_offset_type" value="offsets_absolute"/>\n- <param name="left_column_offset" value="0"/>\n- <param name="right_column_offset" value="0"/>\n- <param name="score_operation" value="min"/>\n- <param name="score_comparison" value=">="/>\n- <param name="score" value="0"/>\n+ <repeat name="fastq_filters">\n+ <conditional name="offset_type">\n+ <param name="base_offset_type" value="offsets_absolute"/>\n+ <param name="left_column_offset" value="0"/>\n+ <param name="right_column_offset" value="0"/>\n+ </conditional>\n+ <param name="score_operation" value="min"/>\n+ <param name="score_comparison" value=">="/>\n+ <param name="score" value="0"/>\n+ </repeat>\n <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />\n </test>\n <!-- Remove all Filter -->\n@@ -176,12 +188,16 @@\n <param name="max_quality" value="0"/>\n <param name="max_num_deviants" value="0"/>\n <param name="paired_end" value="false"/>\n- <param name="base_offset_type" value='..b'\n+ <param name="score_operation" value="min"/>\n+ <param name="score_comparison" value=">="/>\n+ <param name="score" value="1"/>\n+ </repeat>\n <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />\n </test>\n <test>\n@@ -258,12 +282,16 @@\n <param name="max_quality" value="0"/>\n <param name="max_num_deviants" value="0"/>\n <param name="paired_end" value="false"/>\n- <param name="base_offset_type" value="offsets_absolute"/>\n- <param name="left_column_offset" value="1"/>\n- <param name="right_column_offset" value="1"/>\n- <param name="score_operation" value="max"/>\n- <param name="score_comparison" value="<="/>\n- <param name="score" value="92"/>\n+ <repeat name="fastq_filters">\n+ <conditional name="offset_type">\n+ <param name="base_offset_type" value="offsets_absolute"/>\n+ <param name="left_column_offset" value="1"/>\n+ <param name="right_column_offset" value="1"/>\n+ </conditional>\n+ <param name="score_operation" value="max"/>\n+ <param name="score_comparison" value="<="/>\n+ <param name="score" value="92"/>\n+ </repeat>\n <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />\n </test>\n <!-- percent based offsets -->\n@@ -275,12 +303,16 @@\n <param name="max_quality" value="0"/>\n <param name="max_num_deviants" value="0"/>\n <param name="paired_end" value="false"/>\n- <param name="base_offset_type" value="offsets_percent"/>\n- <param name="left_column_offset" value="1.075"/>\n- <param name="right_column_offset" value="1.075"/>\n- <param name="score_operation" value="min"/>\n- <param name="score_comparison" value=">="/>\n- <param name="score" value="1"/>\n+ <repeat name="fastq_filters">\n+ <conditional name="offset_type">\n+ <param name="base_offset_type" value="offsets_percent"/>\n+ <param name="left_column_offset" value="1.075"/>\n+ <param name="right_column_offset" value="1.075"/>\n+ </conditional>\n+ <param name="score_operation" value="min"/>\n+ <param name="score_comparison" value=">="/>\n+ <param name="score" value="1"/>\n+ </repeat>\n <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />\n </test>\n <test>\n@@ -291,12 +323,16 @@\n <param name="max_quality" value="0"/>\n <param name="max_num_deviants" value="0"/>\n <param name="paired_end" value="true"/>\n- <param name="base_offset_type" value="offsets_percent"/>\n- <param name="left_column_offset" value="1"/>\n- <param name="right_column_offset" value="1"/>\n- <param name="score_operation" value="min"/>\n- <param name="score_comparison" value=">="/>\n- <param name="score" value="1"/>\n+ <repeat name="fastq_filters">\n+ <conditional name="offset_type">\n+ <param name="base_offset_type" value="offsets_percent"/>\n+ <param name="left_column_offset" value="1"/>\n+ <param name="right_column_offset" value="1"/>\n+ </conditional>\n+ <param name="score_operation" value="min"/>\n+ <param name="score_comparison" value=">="/>\n+ <param name="score" value="1"/>\n+ </repeat>\n <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />\n </test>\n </tests>\n' |
| b |
| diff -r 144275714590 -r ff7d49ec777f macros.xml --- a/macros.xml Fri Oct 04 10:34:25 2024 +0000 +++ b/macros.xml Sun Nov 23 17:50:05 2025 +0000 |
| b |
| @@ -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> |