| Previous changeset 3:723a93febe89 (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 obistat.xml test-data/input_ngsfilter_extrafile.txt |
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| diff -r 723a93febe89 -r 5f4544915893 macros.xml --- a/macros.xml Mon May 10 19:37:00 2021 +0000 +++ b/macros.xml Wed Mar 20 13:16:41 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 723a93febe89 -r 5f4544915893 obistat.xml --- a/obistat.xml Mon May 10 19:37:00 2021 +0000 +++ b/obistat.xml Wed Mar 20 13:16:41 2024 +0000 |
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| b'@@ -1,147 +1,148 @@\n-<tool id="obi_stat" name="obistat" version="@TOOL_VERSION@" profile="@PROFILE@">\n- <description>computes basic statistics for attribute values</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- obistat\n- --without-progress-bar\n- #for $attribute in $catattributes\n- #if str( $attribute.options_attributespe.options_attributespe_selector) == "key"\n- -c \'$attribute.options_attributespe.options_catattribute_selector\'\n- #end if\n- #if str( $attribute.options_attributespe.options_attributespe_selector) == "python"\n- -c \'${attribute.options_attributespe.attribute}\'\n- #end if\n- #end for\n-\n- #if str( $options_attribute.options_attributebe_selector) == "yes"\n- #if str( $options_attribute.options_attribute_selector) == "min"\n- -m \'$options_attribute.options_uniq_selector\'\n- #end if\n- #if str( $options_attribute.options_attribute_selector) == "max"\n- -M \'$options_attribute.options_uniq_selector\'\n- #end if\n- #if str( $options_attribute.options_attribute_selector) == "mean"\n- -a \'$options_attribute.options_uniq_selector\'\n- #end if\n- #if str( $options_attribute.options_attribute_selector) == "variance"\n- -v \'$options_attribute.options_uniq_selector\'\n- #end if\n- #if str( $options_attribute.options_attribute_selector) == "std"\n- -s \'$options_attribute.options_uniq_selector\'\n- #end if\n- #end if\n- @INPUT_FORMAT@\n- input > \'$output\'\n- ]]></command>\n- <inputs>\n- <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file" />\n- <repeat name="catattributes" title="Category attribute" min="0">\n- <conditional name="options_attributespe">\n- <param name="options_attributespe_selector" type="select" label="How would you specify the category attribute key?" >\n- <option value="key" selected="true">simply by a key of an attribute</option>\n- <option value="python">by a python expression</option>\n- </param>\n- <when value="python">\n- <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." >\n- <expand macro="sanitizer"/>\n- </param>\n- </when>\n- <when value="key">\n- <param name="options_catattribute_selector" type="select" label="Attribute used to categorize the sequence records" >\n- <expand macro="attributes"/>\n- </param>\n- </when>\n- </conditional>\n- </repeat>\n- <conditional name="options_attribute">\n- <param name="options_attributebe_selector" type="select" label="Use a specific option" >\n- <option value="None" selected="true">no</option>\n- <option value="yes">yes</option>\n- </param>\n- <when value="yes">\n- <param name="options_attribute_selector" type="select" label="Select your specific option" >\n- <option value="min" selected="true">min</option>\n- <option value="max">max</option>\n- <option value="mean">mean</option>\n- <option value="variance">variance</option>\n- <option value="std">standard deviation</option>\n- </param>\n- <param name="options_uniq_selector" type="select" label="Attribute to merge" '..b'l="Use a specific option">\r\n+ <option value="None" selected="true">no</option>\r\n+ <option value="yes">yes</option>\r\n+ </param>\r\n+ <when value="yes">\r\n+ <param name="options_attribute_selector" type="select" label="Select your specific option">\r\n+ <option value="min" selected="true">min</option>\r\n+ <option value="max">max</option>\r\n+ <option value="mean">mean</option>\r\n+ <option value="variance">variance</option>\r\n+ <option value="std">standard deviation</option>\r\n+ </param>\r\n+ <param name="options_uniq_selector" type="select" label="Attribute to merge">\r\n+ <expand macro="attributes"/>\r\n+ </param>\r\n+ </when>\r\n+ <when value="None"></when>\r\n+ </conditional>\r\n+ <expand macro="input_format_options_macro"/>\r\n+ </inputs>\r\n+ <outputs>\r\n+ <data format="txt" name="output"/>\r\n+ </outputs>\r\n+ <tests>\r\n+ <test expect_num_outputs="1">\r\n+ <param name="input" value="output_obiannotate.fasta" ftype="fasta"/>\r\n+ <conditional name="catattributes_0|options_attributespe">\r\n+ <param name="options_attributespe_selector" value="key"/>\r\n+ <param name="options_catattribute_selector" value="count" />\r\n+ </conditional>\r\n+ <conditional name="catattributes_1|options_attributespe">\r\n+ <param name="options_attributespe_selector" value="key"/>\r\n+ <param name="options_catattribute_selector" value="merged" />\r\n+ </conditional>\r\n+ <conditional name="options_attribute">\r\n+ <param name="options_attributebe_selector" value="yes"/>\r\n+ <param name="options_attribute_selector" value="min" />\r\n+ <param name="options_uniq_selector" value="seq_length" />\r\n+ </conditional>\r\n+ <output name="output" file="output_obistat.txt" ftype="txt" sort="True"/>\r\n+ </test>\r\n+ <test expect_num_outputs="1">\r\n+ <param name="input" value="output_obiannotate.fasta.gz" ftype="fasta.gz" />\r\n+ <conditional name="catattributes_0|options_attributespe">\r\n+ <param name="options_attributespe_selector" value="key"/>\r\n+ <param name="options_catattribute_selector" value="count" />\r\n+ </conditional>\r\n+ <conditional name="catattributes_1|options_attributespe">\r\n+ <param name="options_attributespe_selector" value="key"/>\r\n+ <param name="options_catattribute_selector" value="merged" />\r\n+ </conditional>\r\n+ <conditional name="options_attribute">\r\n+ <param name="options_attributebe_selector" value="yes"/>\r\n+ <param name="options_attribute_selector" value="min" />\r\n+ <param name="options_uniq_selector" value="seq_length" />\r\n+ </conditional>\r\n+ <output name="output" file="output_obistat.txt" ftype="txt" sort="True"/>\r\n+ </test>\r\n+ </tests>\r\n+ <help><![CDATA[\r\n+\r\n+.. class:: infomark\r\n+\r\n+**What it does**\r\n+\r\n+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:\r\n+\r\n+\\* minimum value (-m option)\r\n+\r\n+\\* maximum value (-M option)\r\n+\r\n+\\* mean value (-a option)\r\n+\r\n+\\* variance (-v option)\r\n+\r\n+\\* standard deviation (-s option)\r\n+\r\n+The result is a contingency table with the different categories in rows, and the computed statistics in columns.\r\n+\r\n+@OBITOOLS_LINK@\r\n+\r\n+ ]]>\r\n+ </help>\r\n+ <expand macro="citation" />\r\n+</tool>\r\n' |
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| diff -r 723a93febe89 -r 5f4544915893 test-data/input_ngsfilter_extrafile.txt --- 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 |
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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 @ |