| Previous changeset 3:5f7003111e32 (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 obitab.xml test-data/input_ngsfilter_extrafile.txt |
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| diff -r 5f7003111e32 -r 4cf47c504672 macros.xml --- a/macros.xml Mon May 10 19:35:19 2021 +0000 +++ b/macros.xml Wed Mar 20 13:17:50 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 5f7003111e32 -r 4cf47c504672 obitab.xml --- a/obitab.xml Mon May 10 19:35:19 2021 +0000 +++ b/obitab.xml Wed Mar 20 13:17:50 2024 +0000 |
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| @@ -1,53 +1,54 @@ -<tool id="obi_tab" name="obitab" version="@TOOL_VERSION@" profile="@PROFILE@"> - <description>converts sequence file to a tabular file</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"/> - <expand macro="stdio"/> - <command><![CDATA[ - @GUNZIP_INPUT@ - - obitab - --without-progress-bar - #if $additional_file - --omit-attribute='$additional_file' - #end if - ${output_seq_option} - ${no_definition_option} - @INPUT_FORMAT@ - input > '$output' - ]]></command> - <inputs> - <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" /> - <param name="output_seq_option" type="boolean" checked="false" truevalue="-o" falsevalue="" label="Do you want to add an extra column?" help="Use this option if you want to add an extra column at the end of the table for the sequence itself"/> - <param name="no_definition_option" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Do you want to remove column containing the sequence definition?" help="Use this option if you want to remove column containing the sequence definition in the output tab file"/> - <param name="additional_file" type="data" optional="true" format="tabular" label="filter attributes from tabular file" /> - <expand macro="input_format_options_macro"/> - </inputs> - <outputs> - <data format="tabular" name="output"/> - </outputs> - <tests> - <test> - <param name="input" value="output_obisort.fastq" /> - <param name="output_seq_option" value="False"/> - <param name="no_definition_option" value="True"/> - <output name="output" file="output_obitab.txt" ftype="tabular"/> - </test> - </tests> - <help><![CDATA[ - - -.. class:: infomark - -**What it does** - -obitab command converts sequence file to a tabular file that can be open by a spreadsheet program or R - -@OBITOOLS_LINK@ - - ]]> - </help> - <expand macro="citation" /> -</tool> \ No newline at end of file +<tool id="obi_tab" name="obitab" version="@TOOL_VERSION@" profile="@PROFILE@"> + <description>converts sequence file to a tabular file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="bio_tools"/> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command><![CDATA[ + @GUNZIP_INPUT@ + + obitab + --without-progress-bar + #if $additional_file + --omit-attribute='$additional_file' + #end if + ${output_seq_option} + ${no_definition_option} + @INPUT_FORMAT@ + input > '$output' + ]]></command> + <inputs> + <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file"/> + <param name="output_seq_option" type="boolean" checked="false" truevalue="-o" falsevalue="" label="Do you want to add an extra column?" help="Use this option if you want to add an extra column at the end of the table for the sequence itself"/> + <param name="no_definition_option" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Do you want to remove column containing the sequence definition?" help="Use this option if you want to remove column containing the sequence definition in the output tab file"/> + <param name="additional_file" type="data" optional="true" format="tabular" label="filter attributes from tabular file"/> + <expand macro="input_format_options_macro"/> + </inputs> + <outputs> + <data format="tabular" name="output"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input" value="output_obisort.fastq" /> + <param name="output_seq_option" value="False"/> + <param name="no_definition_option" value="True"/> + <output name="output" file="output_obitab.txt" ftype="tabular"/> + </test> + </tests> + <help><![CDATA[ + + +.. class:: infomark + +**What it does** + +obitab command converts sequence file to a tabular file that can be open by a spreadsheet program or R + +@OBITOOLS_LINK@ + + ]]> + </help> + <expand macro="citation" /> +</tool> |
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| diff -r 5f7003111e32 -r 4cf47c504672 test-data/input_ngsfilter_extrafile.txt --- a/test-data/input_ngsfilter_extrafile.txt Mon May 10 19:35:19 2021 +0000 +++ b/test-data/input_ngsfilter_extrafile.txt Wed Mar 20 13:17:50 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 @ |