diff obiuniq.xml @ 3:ec215ed98831 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"

--- a/obiuniq.xml	Thu Nov 28 15:52:27 2019 -0500
+++ b/obiuniq.xml	Mon May 10 19:34:29 2021 +0000
@@ -1,92 +1,86 @@
-<tool id="obi_uniq" name="obiuniq" version="@TOOL_VERSION@">
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements"/>
-    <expand macro="stdio"/>
-<command>
-
-    <![CDATA[
-
-    obiuniq
-    #if str( $options_attribute) == "merge"
-        -m '$options_uniq'
-    #else
-        -c '$options_uniq'
-    #end if
-    ${mid}
-    ${prefix}
-    '$input' > '$output'
-
-    ]]>
-
-</command>
-
-<inputs>
-    <param name="input" type="data" format="fasta,fastq" 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" />
-</inputs>
-<outputs>
-    <data format="fasta" name="output" label="output.fasta with ${tool.name} on ${on_string}" />
-</outputs>
-
-<tests>
-   <test>
-       <param name="input" value="output_ngsfilter_error_3.fastq" />
-       <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" />
-       <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" ftype="fasta"/>
-   </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="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>