| Previous changeset 3:f82cefbbcea5 (2021-05-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44 |
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modified:
macros.xml obiannotate.xml test-data/input_ngsfilter_extrafile.txt |
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| diff -r f82cefbbcea5 -r d50dc96e3ce9 macros.xml --- a/macros.xml Mon May 10 19:37:25 2021 +0000 +++ b/macros.xml Wed Mar 20 13:16:14 2024 +0000 |
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| @@ -5,7 +5,11 @@ <requirement type="package" version="@TOOL_VERSION@">obitools</requirement> </requirements> </xml> - + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">obitools</xref> + </xrefs> + </xml> <token name="@TOOL_VERSION@">1.2.13</token> <token name="@PROFILE@">21.01</token> |
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| diff -r f82cefbbcea5 -r d50dc96e3ce9 obiannotate.xml --- a/obiannotate.xml Mon May 10 19:37:25 2021 +0000 +++ b/obiannotate.xml Wed Mar 20 13:16:14 2024 +0000 |
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| b'@@ -1,175 +1,176 @@\n-<tool id="obi_annotate" name="obiannotate" version="@TOOL_VERSION@" profile="@PROFILE@">\n- <description>Adds/Edits sequence record annotations</description>\n- <macros>\n- <import>macros.xml</import>\n- </macros>\n- <expand macro="requirements"/>\n- <expand macro="stdio"/>\n- <command><![CDATA[\n- @GUNZIP_INPUT@\n-\n- obiannotate\n- --without-progress-bar\n- ${seqrank}\n-\n- #if $rename_tag.old_name and $rename_tag.new_name\n- -R \'$rename_tag.old_name\':\'$rename_tag.new_name\'\n- #end if\n-\n- #if $deletetag_key\n- --delete-tag=\'$deletetag_key\'\n- #end if\n-\n- #if $set_tag.key and $set_tag.pythonexpression\n- -S \'$set_tag.key\':\'$set_tag.pythonexpression\'\n- #end if\n-\n- #if $taglist\n- --tag-list=\'$taglist\'\n- #end if\n-\n- #if $setid_pythonexpression\n- --set-identifier=\'$setid_pythonexpression\'\n- #end if\n-\n- #if $pythonexpression\n- --run=\'$pythonexpression\'\n- #end if\n-\n- #if $setsequence_pythonexpression\n- --set-sequence=\'$setsequence_pythonexpression\'\n- #end if\n-\n- #if $setdefinition_pythonexpression\n- --set-definition=\'$setdefinition_pythonexpression\'\n- #end if\n-\n- #if $key_selector.key\n- --keep=\'$key_selector.key\'\n- #end if\n- #if $key_selector.key2\n- --keep=\'$key_selector.key2\'\n- #end if\n- #if $key_selector.key3\n- --keep=\'$key_selector.key3\'\n- #end if\n- #if $key_selector.key4\n- --keep=\'$key_selector.key4\'\n- #end if\n- #if $key_selector.key5\n- --keep=\'$key_selector.key5\'\n- #end if\n-\n- ${length}\n- ${clearbool}\n- ${uniqid}\n-\n- #if $rankname\n- --with-taxon-at-rank=\'$rankname\'\n- #end if\n-\n- #if $mclfile\n- --mcl=\'$mclfile\'\n- #end if\n- @INPUT_FORMAT@\n- @OUT_FORMAT@\n- input\n- @GZIP_OUTPUT@\n- > \'$output\'\n- \n- @GENERATE_GALAXY_JSON@\n- ]]></command>\n-\n- <inputs>\n- <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file" />\n- <param name="seqrank" type="boolean" label="Add a new attribute seq_rank" truevalue="--seq-rank" falsevalue="" help="Use this option if you want to add a new attribute named seq_rank to the sequence record indicating its entry number in the sequence file" />\n- <section name="rename_tag" title="Rename attribute" expanded="False">\n- <param name="old_name" type="text" label="old name" optional="true"/>\n- <param name="new_name" type="text" label="new name" optional="true"/>\n- </section>\n- <param name="deletetag_key" type="text" label="Delete attribute" optional="true" help="Use this option if you want to delete attribute named ATTRIBUTE_NAME.When this attribute is missing, the sequence record is skipped and the next one is examined"/>\n-\n- <section name="set_tag" title="Create a new attribute" expanded="False">\n- <param name="key" type="text" label="key" optional="true"/>\n- <param name="pythonexpression" type="text" label="python expression" optional="true"/>\n- </section>\n-\n- <param name="taglist" type="data" optional="true" format="txt,tabular" label="Use a tag list" help="file containing identifiers of sequences to select" />\n-\n- <param name="setid_pythonexpression" type="text" label="Set sequence record identifier with a value" help="Use this option if you want to set sequence record identifier with a value computed from PYTHON_EXPRESSION" />\n-\n- <param name="pythonexpression" type="text" label="Run a PYTHON_EXPRESSION on each selected sequence" optional="true" help="Use this option if you want to run a PYTHON_EXPRESSION on each selected sequence"/>\n-\n- <param name="setsequence_pyt'..b'nt to change the sequence itself with a value computed from PYTHON_EXPRESSION"/>\r\n+\r\n+ <param name="setdefinition_pythonexpression" type="text" label="Set sequence definition with a value computed" help="Use this option if you want to set sequence definition with a value computed from PYTHON_EXPRESSION"/>\r\n+\r\n+ <param name="clearbool" type="boolean" label="Clear all attributes associated to the sequence records" truevalue="--clear" falsevalue="" help="Use this option if you want to clear all attributes associated to the sequence records" />\r\n+\r\n+ <section name="key_selector" title="Keep only attribute with key" expanded="False">\r\n+ <param name="key" type="text" label="key" optional="true" />\r\n+ <param name="key2" type="text" label="if you want to specify a second key" optional="true" />\r\n+ <param name="key3" type="text" label="if you want to specify a third key" optional="true" />\r\n+ <param name="key4" type="text" label="if you want to specify a fourth key" optional="true" />\r\n+ <param name="key5" type="text" label="if you want to specify a fifth key" optional="true" />\r\n+ </section>\r\n+\r\n+ <param name="length" type="boolean" label="Use the length option?" truevalue="--length" falsevalue="" help="Use this option if you want to add attribute with seq_length as a key and sequence length as a value" />\r\n+\r\n+ <param name="rankname" type="text" label="Add taxonomic annotation" help="Use this option if you want to add taxonomic annotation at taxonomic rank RANK_NAME"/>\r\n+\r\n+ <param name="mclfile" optional="true" type="data" format="txt,tabular" label="mcl file" help="use this option if you want to add a new attribute containing the number of the cluster the sequence record was assigned to, as indicated in file MCLFILE" />\r\n+\r\n+ <param name="uniqid" type="boolean" label="Force sequence record ids to be unique" truevalue="--uniq-id" falsevalue="" help="Use this option if you want to force sequence record ids to be unique" />\r\n+ <expand macro="input_format_options_macro"/>\r\n+ <expand macro="out_format_macro"/>\r\n+ </inputs>\r\n+ <outputs>\r\n+ <data name="output" format="auto"/>\r\n+ </outputs>\r\n+ <tests>\r\n+ <test expect_num_outputs="1">\r\n+ <param name="input" value="output_obiuniq.fasta" ftype="fasta"/>\r\n+ <section name="key_selector">\r\n+ <param name="key" value="count"/>\r\n+ <param name="key2" value="merged_sample"/>\r\n+ </section>\r\n+ <param name="uniqid" value="true"/>\r\n+ <param name="clearbool" value="true"/>\r\n+ <param name="length" value="true"/>\r\n+ <param name="seqrank" value="true"/>\r\n+\r\n+ <output name="output" file="output_obiannotate.fasta" ftype="fasta"/>\r\n+ </test>\r\n+ <test expect_num_outputs="1">\r\n+ <param name="input" value="output_obiuniq.fasta.gz" ftype="fasta.gz"/>\r\n+ <section name="key_selector">\r\n+ <param name="key" value="count"/>\r\n+ <param name="key2" value="merged_sample"/>\r\n+ </section>\r\n+ <param name="uniqid" value="true"/>\r\n+ <param name="clearbool" value="true"/>\r\n+ <param name="length" value="true"/>\r\n+ <param name="seqrank" value="true"/>\r\n+ <output name="output" file="output_obiannotate.fasta.gz" ftype="fasta.gz" decompress="true"/>\r\n+ </test>\r\n+ <!-- TODO fastq input test -->\r\n+ </tests>\r\n+\r\n+ <help><![CDATA[\r\n+\r\n+.. class:: infomark\r\n+\r\n+**What it does**\r\n+\r\n+`obiannotate` is the command that allows adding/modifying/removing annotation attributes attached to sequence records.\r\n+\r\n+Once such attributes are added, they can be used by the other OBITools commands for filtering purposes or for statistics computing.\r\n+\r\n+@OBITOOLS_LINK@\r\n+\r\n+]]>\r\n+\r\n+ </help>\r\n+ <expand macro="citation" />\r\n+</tool>\r\n' |
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| diff -r f82cefbbcea5 -r d50dc96e3ce9 test-data/input_ngsfilter_extrafile.txt --- a/test-data/input_ngsfilter_extrafile.txt Mon May 10 19:37:25 2021 +0000 +++ b/test-data/input_ngsfilter_extrafile.txt Wed Mar 20 13:16:14 2024 +0000 |
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| @@ -1,4 +1,4 @@ -wolf_diet 13a_F730603 aattaac TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ -wolf_diet 15a_F730814 gaagtag TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ -wolf_diet 26a_F040644 gaatatc TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ -wolf_diet 29a_F260619 gcctcct TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ +wolf_diet 13a_F730603 aattaac TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ +wolf_diet 15a_F730814 gaagtag TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ +wolf_diet 26a_F040644 gaatatc TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ +wolf_diet 29a_F260619 gcctcct TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ |