Mercurial > repos > iuc > obi_stat
changeset 4:5f4544915893 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
| author | iuc |
|---|---|
| date | Wed, 20 Mar 2024 13:16:41 +0000 |
| parents | 723a93febe89 |
| children | |
| files | macros.xml obistat.xml test-data/input_ngsfilter_extrafile.txt |
| diffstat | 3 files changed, 157 insertions(+), 152 deletions(-) [+] |
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--- a/macros.xml Mon May 10 19:37:00 2021 +0000 +++ b/macros.xml Wed Mar 20 13:16:41 2024 +0000 @@ -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>
--- a/obistat.xml Mon May 10 19:37:00 2021 +0000 +++ b/obistat.xml Wed Mar 20 13:16:41 2024 +0000 @@ -1,147 +1,148 @@ -<tool id="obi_stat" name="obistat" version="@TOOL_VERSION@" profile="@PROFILE@"> - <description>computes basic statistics for attribute values</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"/> - <expand macro="stdio"/> - <command><![CDATA[ - @GUNZIP_INPUT@ - - obistat - --without-progress-bar - #for $attribute in $catattributes - #if str( $attribute.options_attributespe.options_attributespe_selector) == "key" - -c '$attribute.options_attributespe.options_catattribute_selector' - #end if - #if str( $attribute.options_attributespe.options_attributespe_selector) == "python" - -c '${attribute.options_attributespe.attribute}' - #end if - #end for - - #if str( $options_attribute.options_attributebe_selector) == "yes" - #if str( $options_attribute.options_attribute_selector) == "min" - -m '$options_attribute.options_uniq_selector' - #end if - #if str( $options_attribute.options_attribute_selector) == "max" - -M '$options_attribute.options_uniq_selector' - #end if - #if str( $options_attribute.options_attribute_selector) == "mean" - -a '$options_attribute.options_uniq_selector' - #end if - #if str( $options_attribute.options_attribute_selector) == "variance" - -v '$options_attribute.options_uniq_selector' - #end if - #if str( $options_attribute.options_attribute_selector) == "std" - -s '$options_attribute.options_uniq_selector' - #end if - #end if - @INPUT_FORMAT@ - input > '$output' - ]]></command> - <inputs> - <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file" /> - <repeat name="catattributes" title="Category attribute" min="0"> - <conditional name="options_attributespe"> - <param name="options_attributespe_selector" type="select" label="How would you specify the category attribute key?" > - <option value="key" selected="true">simply by a key of an attribute</option> - <option value="python">by a python expression</option> - </param> - <when value="python"> - <param name="attribute" type="text" label="Regular expression pattern matched against the attributes of the sequence record. the value of this attribute is of the form : key:regular_pattern. The pattern is case sensitive." > - <expand macro="sanitizer"/> - </param> - </when> - <when value="key"> - <param name="options_catattribute_selector" type="select" label="Attribute used to categorize the sequence records" > - <expand macro="attributes"/> - </param> - </when> - </conditional> - </repeat> - <conditional name="options_attribute"> - <param name="options_attributebe_selector" type="select" label="Use a specific option" > - <option value="None" selected="true">no</option> - <option value="yes">yes</option> - </param> - <when value="yes"> - <param name="options_attribute_selector" type="select" label="Select your specific option" > - <option value="min" selected="true">min</option> - <option value="max">max</option> - <option value="mean">mean</option> - <option value="variance">variance</option> - <option value="std">standard deviation</option> - </param> - <param name="options_uniq_selector" type="select" label="Attribute to merge" > - <expand macro="attributes"/> - </param> - </when> - <when value="None"></when> - </conditional> - <expand macro="input_format_options_macro"/> - </inputs> - <outputs> - <data format="txt" name="output"/> - </outputs> - <tests> - <test> - <param name="input" value="output_obiannotate.fasta" ftype="fasta"/> - <conditional name="catattributes_0|options_attributespe"> - <param name="options_attributespe_selector" value="key"/> - <param name="options_catattribute_selector" value="count" /> - </conditional> - <conditional name="catattributes_1|options_attributespe"> - <param name="options_attributespe_selector" value="key"/> - <param name="options_catattribute_selector" value="merged" /> - </conditional> - <conditional name="options_attribute"> - <param name="options_attributebe_selector" value="yes"/> - <param name="options_attribute_selector" value="min" /> - <param name="options_uniq_selector" value="seq_length" /> - </conditional> - <output name="output" file="output_obistat.txt" ftype="txt" sort="True"/> - </test> - <test> - <param name="input" value="output_obiannotate.fasta.gz" ftype="fasta.gz" /> - <conditional name="catattributes_0|options_attributespe"> - <param name="options_attributespe_selector" value="key"/> - <param name="options_catattribute_selector" value="count" /> - </conditional> - <conditional name="catattributes_1|options_attributespe"> - <param name="options_attributespe_selector" value="key"/> - <param name="options_catattribute_selector" value="merged" /> - </conditional> - <conditional name="options_attribute"> - <param name="options_attributebe_selector" value="yes"/> - <param name="options_attribute_selector" value="min" /> - <param name="options_uniq_selector" value="seq_length" /> - </conditional> - <output name="output" file="output_obistat.txt" ftype="txt" sort="True"/> - </test> - </tests> - <help><![CDATA[ - -.. class:: infomark - -**What it does** - -stats computes basic statistics for attribute values of sequence records. The sequence records can be categorized or not using one or several -c options. By default, only the number of sequence records and the total count are computed for each category. Additional statistics can be computed for attribute values in each category, like: - -\* minimum value (-m option) - -\* maximum value (-M option) - -\* mean value (-a option) - -\* variance (-v option) - -\* standard deviation (-s option) - -The result is a contingency table with the different categories in rows, and the computed statistics in columns. - -@OBITOOLS_LINK@ - - ]]> - </help> - <expand macro="citation" /> -</tool> +<tool id="obi_stat" name="obistat" version="@TOOL_VERSION@" profile="@PROFILE@"> + <description>computes basic statistics for attribute values</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="bio_tools"/> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command><![CDATA[ + @GUNZIP_INPUT@ + + obistat + --without-progress-bar + #for $attribute in $catattributes + #if str( $attribute.options_attributespe.options_attributespe_selector) == "key" + -c '$attribute.options_attributespe.options_catattribute_selector' + #end if + #if str( $attribute.options_attributespe.options_attributespe_selector) == "python" + -c '${attribute.options_attributespe.attribute}' + #end if + #end for + + #if str( $options_attribute.options_attributebe_selector) == "yes" + #if str( $options_attribute.options_attribute_selector) == "min" + -m '$options_attribute.options_uniq_selector' + #end if + #if str( $options_attribute.options_attribute_selector) == "max" + -M '$options_attribute.options_uniq_selector' + #end if + #if str( $options_attribute.options_attribute_selector) == "mean" + -a '$options_attribute.options_uniq_selector' + #end if + #if str( $options_attribute.options_attribute_selector) == "variance" + -v '$options_attribute.options_uniq_selector' + #end if + #if str( $options_attribute.options_attribute_selector) == "std" + -s '$options_attribute.options_uniq_selector' + #end if + #end if + @INPUT_FORMAT@ + input > '$output' + ]]></command> + <inputs> + <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file"/> + <repeat name="catattributes" title="Category attribute" min="0"> + <conditional name="options_attributespe"> + <param name="options_attributespe_selector" type="select" label="How would you specify the category attribute key?"> + <option value="key" selected="true">simply by a key of an attribute</option> + <option value="python">by a python expression</option> + </param> + <when value="python"> + <param name="attribute" type="text" label="Regular expression pattern matched against the attributes of the sequence record. the value of this attribute is of the form : key:regular_pattern. The pattern is case sensitive."> + <expand macro="sanitizer"/> + </param> + </when> + <when value="key"> + <param name="options_catattribute_selector" type="select" label="Attribute used to categorize the sequence records"> + <expand macro="attributes"/> + </param> + </when> + </conditional> + </repeat> + <conditional name="options_attribute"> + <param name="options_attributebe_selector" type="select" label="Use a specific option"> + <option value="None" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="yes"> + <param name="options_attribute_selector" type="select" label="Select your specific option"> + <option value="min" selected="true">min</option> + <option value="max">max</option> + <option value="mean">mean</option> + <option value="variance">variance</option> + <option value="std">standard deviation</option> + </param> + <param name="options_uniq_selector" type="select" label="Attribute to merge"> + <expand macro="attributes"/> + </param> + </when> + <when value="None"></when> + </conditional> + <expand macro="input_format_options_macro"/> + </inputs> + <outputs> + <data format="txt" name="output"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input" value="output_obiannotate.fasta" ftype="fasta"/> + <conditional name="catattributes_0|options_attributespe"> + <param name="options_attributespe_selector" value="key"/> + <param name="options_catattribute_selector" value="count" /> + </conditional> + <conditional name="catattributes_1|options_attributespe"> + <param name="options_attributespe_selector" value="key"/> + <param name="options_catattribute_selector" value="merged" /> + </conditional> + <conditional name="options_attribute"> + <param name="options_attributebe_selector" value="yes"/> + <param name="options_attribute_selector" value="min" /> + <param name="options_uniq_selector" value="seq_length" /> + </conditional> + <output name="output" file="output_obistat.txt" ftype="txt" sort="True"/> + </test> + <test expect_num_outputs="1"> + <param name="input" value="output_obiannotate.fasta.gz" ftype="fasta.gz" /> + <conditional name="catattributes_0|options_attributespe"> + <param name="options_attributespe_selector" value="key"/> + <param name="options_catattribute_selector" value="count" /> + </conditional> + <conditional name="catattributes_1|options_attributespe"> + <param name="options_attributespe_selector" value="key"/> + <param name="options_catattribute_selector" value="merged" /> + </conditional> + <conditional name="options_attribute"> + <param name="options_attributebe_selector" value="yes"/> + <param name="options_attribute_selector" value="min" /> + <param name="options_uniq_selector" value="seq_length" /> + </conditional> + <output name="output" file="output_obistat.txt" ftype="txt" sort="True"/> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +stats computes basic statistics for attribute values of sequence records. The sequence records can be categorized or not using one or several -c options. By default, only the number of sequence records and the total count are computed for each category. Additional statistics can be computed for attribute values in each category, like: + +\* minimum value (-m option) + +\* maximum value (-M option) + +\* mean value (-a option) + +\* variance (-v option) + +\* standard deviation (-s option) + +The result is a contingency table with the different categories in rows, and the computed statistics in columns. + +@OBITOOLS_LINK@ + + ]]> + </help> + <expand macro="citation" /> +</tool>
--- a/test-data/input_ngsfilter_extrafile.txt Mon May 10 19:37:00 2021 +0000 +++ b/test-data/input_ngsfilter_extrafile.txt Wed Mar 20 13:16:41 2024 +0000 @@ -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 @