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changeset 4:d4bea99366f9 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
author iuc
date Wed, 20 Mar 2024 13:16:55 +0000
parents ec215ed98831
children
files macros.xml obiuniq.xml test-data/input_ngsfilter_extrafile.txt
diffstat 3 files changed, 100 insertions(+), 91 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Mon May 10 19:34:29 2021 +0000
+++ b/macros.xml	Wed Mar 20 13:16:55 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/obiuniq.xml	Mon May 10 19:34:29 2021 +0000
+++ b/obiuniq.xml	Wed Mar 20 13:16:55 2024 +0000
@@ -1,86 +1,91 @@
-<tool id="obi_uniq" name="obiuniq" version="@TOOL_VERSION@" profile="@PROFILE@">
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements"/>
-    <expand macro="stdio"/>
-    <command><![CDATA[
-    @GUNZIP_INPUT@
-
-    obiuniq
-    --without-progress-bar
-    #if str( $options_attribute) == "merge"
-        -m '$options_uniq'
-    #else
-        -c '$options_uniq'
-    #end if
-    ${mid}
-    ${prefix}
-    @INPUT_FORMAT@
-    input
-    @GZIP_OUTPUT@
-    > '$output'
-    @GENERATE_GALAXY_JSON@
-    ]]></command>
-    <inputs>
-        <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file" />
-        <param name="options_uniq" type="select" label="Attribute to merge" >
-            <expand macro="attributes"/>
-        </param>
-        <param name="options_attribute" type="select" label="Use specific option" >
-            <option value="merge" selected="true">merge</option>
-            <option value="category_attribute">category_attribute</option>
-        </param>
-        <param name="mid" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Add a merged attribute containing the list of sequence record ids merged within this group" />
-    	<param name="prefix" type="boolean" checked="false" truevalue="-p" falsevalue="" label="Dereplicate through a prefix matching" />
-        <expand macro="input_format_options_macro"/>
-    </inputs>
-    <outputs>
-        <data format="auto" name="output"/>
-    </outputs>
-    <tests>
-       <test>
-           <param name="input" value="output_ngsfilter_error_3.fastq" ftype="fastqsanger"/>
-           <param name="options_uniq" value="sample" />
-           <param name="options_attribute" value="merge" />
-           <param name="mid" value="False" />
-           <param name="prefix" value="False" />
-           <output name="output" file="output_obiuniq.fasta" ftype="fasta"/>
-       </test>
-       <test>
-           <param name="input" value="output_ngsfilter_error_3.fastq.gz" ftype="fastqsanger.gz"/>
-           <param name="options_uniq" value="family" />
-           <param name="options_attribute" value="category_attribute" />
-           <param name="mid" value="True" />
-           <param name="prefix" value="True" />
-           <output name="output" file="output_obiuniq_family.fasta.gz" ftype="fasta.gz" decompress="true"/>
-       </test>
-    </tests>
-    <help><![CDATA[
-    .. class:: infomark
-
-    **What it does**
-
-    The obiuniq command is in some way analog to the standard Unix uniq -c command.
-
-    Instead of working text line by text line as the standard Unix tool, the processing is done on sequence records.
-
-    A sequence record is a complex object composed of an identifier, a set of attributes (key=value), a definition, and the sequence itself.
-
-    The obiuniq command groups together sequence records. Then, for each group, a sequence record is printed.
-
-    A group is defined by the sequence and optionally by the values of a set of attributes specified with the -c option.
-
-    As the identifier, the set of attributes (key=value) and the definition of the sequence records that are grouped together may be different, two options (-m and -i) allow refining how these parts of the records are reported.
-
-    \*  By default, only attributes with identical values within a group of sequence records are kept.
-
-    \*  A count attribute is set to the total number of sequence records for each group.
-
-    \*  For each attribute specified by the -m option, a new attribute whose key is prefixed by merged_ is created. These new attributes contain the number of times each value occurs within the group of sequence records.
-
-
-    @OBITOOLS_LINK@
-    ]]></help>
-    <expand macro="citation" />
-</tool>
+<tool id="obi_uniq" name="obiuniq" version="@TOOL_VERSION@" profile="@PROFILE@">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+    @GUNZIP_INPUT@
+
+    obiuniq
+    --without-progress-bar
+    #if str( $options_attribute) == "merge"
+        -m '$options_uniq'
+    #else
+        -c '$options_uniq'
+    #end if
+    ${mid}
+    ${prefix}
+    @INPUT_FORMAT@
+    input
+    @GZIP_OUTPUT@
+    > '$output'
+    @GENERATE_GALAXY_JSON@
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file"/>
+        <param name="options_uniq" type="select" label="Attribute to merge">
+            <expand macro="attributes"/>
+        </param>
+        <param name="options_attribute" type="select" label="Use specific option">
+            <option value="merge" selected="true">merge</option>
+            <option value="category_attribute">category_attribute</option>
+        </param>
+        <param name="mid" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Add a merged attribute containing the list of sequence record ids merged within this group"/>
+    	<param name="prefix" type="boolean" checked="false" truevalue="-p" falsevalue="" label="Dereplicate through a prefix matching"/>
+        <expand macro="input_format_options_macro"/>
+    </inputs>
+    <outputs>
+        <data format="auto" name="output"/>
+    </outputs>
+    <tests>
+       <test expect_num_outputs="1">
+           <param name="input" value="output_ngsfilter_error_3.fastq" ftype="fastqsanger"/>
+           <param name="options_uniq" value="sample"/>
+           <param name="options_attribute" value="merge"/>
+           <param name="mid" value="False"/>
+           <param name="prefix" value="False"/>
+           <output name="output" file="output_obiuniq.fasta" ftype="fasta"/>
+       </test>
+       <test expect_num_outputs="1">
+           <param name="input" value="output_ngsfilter_error_3.fastq.gz" ftype="fastqsanger.gz"/>
+           <param name="options_uniq" value="family"/>
+           <param name="options_attribute" value="category_attribute"/>
+           <param name="mid" value="True"/>
+           <param name="prefix" value="True"/>
+           <output name="output" file="output_obiuniq_family.fasta.gz" ftype="fasta.gz" decompress="true"/>
+       </test>
+    </tests>
+
+    <help><![CDATA[
+    
+    .. class:: infomark
+
+    **What it does**
+
+    The obiuniq command is in some way analog to the standard Unix uniq -c command.
+
+    Instead of working text line by text line as the standard Unix tool, the processing is done on sequence records.
+
+    A sequence record is a complex object composed of an identifier, a set of attributes (key=value), a definition, and the sequence itself.
+
+    The obiuniq command groups together sequence records. Then, for each group, a sequence record is printed.
+
+    A group is defined by the sequence and optionally by the values of a set of attributes specified with the -c option.
+
+    As the identifier, the set of attributes (key=value) and the definition of the sequence records that are grouped together may be different, two options (-m and -i) allow refining how these parts of the records are reported.
+
+    \* By default, only attributes with identical values within a group of sequence records are kept.
+
+    \*  A count attribute is set to the total number of sequence records for each group.
+
+    \*  For each attribute specified by the -m option, a new attribute whose key is prefixed by merged is created. These new attributes contain the number of times each value occurs within the group of sequence records.
+
+
+    @OBITOOLS_LINK@
+    ]]>
+    
+    </help>
+    <expand macro="citation" />
+</tool>
--- a/test-data/input_ngsfilter_extrafile.txt	Mon May 10 19:34:29 2021 +0000
+++ b/test-data/input_ngsfilter_extrafile.txt	Wed Mar 20 13:16:55 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	@