| Previous changeset 3:374fd9feb032 (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 obiconvert.xml test-data/input_ngsfilter_extrafile.txt |
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| diff -r 374fd9feb032 -r e328ced6cf0a macros.xml --- a/macros.xml Mon May 10 19:36:34 2021 +0000 +++ b/macros.xml Wed Mar 20 13:15:46 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 374fd9feb032 -r e328ced6cf0a obiconvert.xml --- a/obiconvert.xml Mon May 10 19:36:34 2021 +0000 +++ b/obiconvert.xml Wed Mar 20 13:15:46 2024 +0000 |
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| @@ -1,98 +1,99 @@ -<tool id="obi_convert" name="obiconvert" version="@TOOL_VERSION@" profile="@PROFILE@"> - <description>converts sequence files to different output formats</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"/> - <expand macro="stdio"/> - <command><![CDATA[ - @GUNZIP_INPUT@ - - obiconvert - #if $db - -d '$db' - #end if - #if $tax - -t '$tax' - #end if - @INPUT_FORMAT@ - @OUT_FORMAT@ - ${uppercase} - ${ecopcrdb} - #if str( $ecopcrdb) == "--ecopcrdb" - --ecopcrdb-output=${ecopcrdb_output} - #end if - input - @GZIP_OUTPUT@ - > '${output}' - @GENERATE_GALAXY_JSON@ - ]]></command> - <inputs> - <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" help="database used for the in silico PCR. The database must be in the ecoPCR format (for example output of obiconvert)" /> - <param name="db" type="data" optional="true" format="txt,tabular" label="ecoPCR taxonomy database" /> - <param name="tax" type="data" optional="true" format="txt,tabular" label="NCBI taxonomy dump repository"/> - <expand macro="input_format_options_macro"/> - <expand macro="out_format_macro"/> - <param name="ecopcrdb" type="boolean" truevalue="--ecopcrdb" falsevalue="" label="Do you want to create an ecoPCR database from sequence records results?" help="Use this option if you want to generate an ecoPCR database output file" /> - <param name="uppercase" type="boolean" truevalue="--uppercase" falsevalue="" label="Do you want to print sequences in upper case?" /> - </inputs> - <outputs> - <data format="txt" name="ecopcrdb_output" label="${tool.name} on ${on_string}: ecopcrdb"> - <filter>ecopcrdb == True</filter> - </data> - <data format="auto" name="output"/> - </outputs> - <tests> - <test> - <param name="input" value="output_obisort.fasta" /> - <param name="options_inputtype" value="--fasta"/> - <param name="options_seqtype" value="--nuc"/> - <param name="out_format" value="fasta"/> - <param name="ecopcrdb" value="false"/> - <param name="uppercase" value="true"/> - <output name="output" file="output_obiconvert.fasta" ftype="fasta"/> - </test> - </tests> - <help><![CDATA[ - -.. class:: infomark - -**What it does** - -obiconvert converts sequence files to different output formats. See the documentation for more details on the different formats. - -Input files can be in : - -fasta format - -extended OBITools fasta format - -Sanger fastq format - -Solexa fastq format - -ecoPCR format - -ecoPCR database format - -GenBank format - -EMBL format - -obiconvert converts those files to the : - -extended OBITools fasta format - -Sanger fastq format - -ecoPCR database format - -If no file name is specified, data is read from standard input. - -@OBITOOLS_LINK@ - - ]]> - - </help> - <expand macro="citation" /> -</tool> +<tool id="obi_convert" name="obiconvert" version="@TOOL_VERSION@" profile="@PROFILE@"> + <description>converts sequence files to different output formats</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="bio_tools"/> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command><![CDATA[ + @GUNZIP_INPUT@ + + obiconvert + #if $db + -d '$db' + #end if + #if $tax + -t '$tax' + #end if + @INPUT_FORMAT@ + @OUT_FORMAT@ + ${uppercase} + ${ecopcrdb} + #if str( $ecopcrdb) == "--ecopcrdb" + --ecopcrdb-output=${ecopcrdb_output} + #end if + input + @GZIP_OUTPUT@ + > '${output}' + @GENERATE_GALAXY_JSON@ + ]]></command> + <inputs> + <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" help="database used for the in silico PCR. The database must be in the ecoPCR format (for example output of obiconvert)"/> + <param name="db" type="data" optional="true" format="txt,tabular" label="ecoPCR taxonomy database"/> + <param name="tax" type="data" optional="true" format="txt,tabular" label="NCBI taxonomy dump repository"/> + <expand macro="input_format_options_macro"/> + <expand macro="out_format_macro"/> + <param name="ecopcrdb" type="boolean" truevalue="--ecopcrdb" falsevalue="" label="Do you want to create an ecoPCR database from sequence records results?" help="Use this option if you want to generate an ecoPCR database output file"/> + <param name="uppercase" type="boolean" truevalue="--uppercase" falsevalue="" label="Do you want to print sequences in upper case?"/> + </inputs> + <outputs> + <data format="txt" name="ecopcrdb_output" label="${tool.name} on ${on_string}: ecopcrdb"> + <filter>ecopcrdb == True</filter> + </data> + <data format="auto" name="output"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input" value="output_obisort.fasta" /> + <param name="options_inputtype" value="--fasta"/> + <param name="options_seqtype" value="--nuc"/> + <param name="out_format" value="fasta"/> + <param name="ecopcrdb" value="false"/> + <param name="uppercase" value="true"/> + <output name="output" file="output_obiconvert.fasta" ftype="fasta"/> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +obiconvert converts sequence files to different output formats. See the documentation for more details on the different formats. + +Input files can be in : + +fasta format + +extended OBITools fasta format + +Sanger fastq format + +Solexa fastq format + +ecoPCR format + +ecoPCR database format + +GenBank format + +EMBL format + +obiconvert converts those files to the : + +extended OBITools fasta format + +Sanger fastq format + +ecoPCR database format + +If no file name is specified, data is read from standard input. + +@OBITOOLS_LINK@ + + ]]> + + </help> + <expand macro="citation" /> +</tool> |
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| diff -r 374fd9feb032 -r e328ced6cf0a test-data/input_ngsfilter_extrafile.txt --- a/test-data/input_ngsfilter_extrafile.txt Mon May 10 19:36:34 2021 +0000 +++ b/test-data/input_ngsfilter_extrafile.txt Wed Mar 20 13:15:46 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 @ |