diff obitab.xml.orig @ 4:d0f6ac976373 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/obitab.xml.orig	Wed Sep 01 07:49:38 2021 +0000
@@ -0,0 +1,123 @@
+<<<<<<< HEAD
+<tool id="obi_tab" name="obitab" version="@TOOL_VERSION@" profile="@PROFILE@">
+    <description>converts sequence file to a tabular file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+        @GUNZIP_INPUT@
+        
+        obitab
+        --without-progress-bar
+        #if $additional_file
+            --omit-attribute='$additional_file'
+        #end if
+        ${output_seq_option}
+        ${no_definition_option}
+        @INPUT_FORMAT@
+        input > '$output'
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" />
+        <param name="output_seq_option" type="boolean" checked="false" truevalue="-o" falsevalue="" label="Do you want to add an extra column?" help="Use this option if you want to add an extra column at the end of the table for the sequence itself"/>
+        <param name="no_definition_option" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Do you want to remove column containing the sequence definition?" help="Use this option if you want to remove column containing the sequence definition in the output tab file"/>
+        <param name="additional_file" type="data" optional="true" format="tabular" label="filter attributes from tabular file" />
+        <expand macro="input_format_options_macro"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="output_obisort.fastq" />
+            <param name="output_seq_option" value="False"/>
+            <param name="no_definition_option" value="True"/>
+            <output name="output" file="output_obitab.txt" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+
+.. class:: infomark
+
+**What it does**
+
+obitab command converts sequence file to a tabular file that can be open by a spreadsheet program or R
+
+@OBITOOLS_LINK@
+
+    ]]>
+    </help>
+    <expand macro="citation" />
+</tool>
+=======
+<tool id="obi_tab" name="obitab" version="@TOOL_VERSION@">
+    <description>converts sequence file to a tabular file that can be open by a spreadsheet program or R</description>
+    <expand macro="bio_tools"/>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <command>
+
+        <![CDATA[
+        obitab
+        #if $additional_file
+            --omit-attribute='$additional_file'
+        #end if
+        ${output_seq_option}
+        ${no_definition_option}
+        ${options_inputtype}
+        ${options_seqtype}
+
+        '$input' > '$output'
+        ]]>
+
+    </command>
+
+    <inputs>
+        <param name="input" type="data" format="fastq,fasta,txt,tabular" label="Input sequences file" />
+        <param name="output_seq_option" type="boolean" checked="false" truevalue="-o" falsevalue="" label="Do you want to add an extra column?" help="Use this option if you want to add an extra column at the end of the table for the sequence itself"/>
+        <param name="no_definition_option" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Do you want to remove column containing the sequence definition?" help="Use this option if you want to remove column containing the sequence definition in the output tab file"/>
+        <param name="additional_file" type="data" optional="true" format="tabular" label="filter attributes from tabular file" />
+        <param name="options_inputtype" type="select" label="Specify the input datatype">
+            <expand macro="inputtype"/>
+        </param>
+        <param name="options_seqtype" type="select" label="Specify the sequence datatype" >
+            <option value="--nuc" selected="true">nucleic</option>
+            <option value="--prot">protein</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" label="output.tabular with ${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="output_obisort.fastq" />
+            <param name="output_seq_option" value="False"/>
+            <param name="no_definition_option" value="True"/>
+            <param name="options_inputtype" value="fasta"/>
+            <param name="options_seqtype" value="--prot"/>
+            <output name="output" file="output_obitab.txt" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+
+.. class:: infomark
+
+**What it does**
+
+obitab command converts sequence file to a tabular file that can be open by a spreadsheet program or R
+
+@OBITOOLS_LINK@
+
+    ]]>
+    </help>
+    <expand macro="citation" />
+    </tool>
+>>>>>>> 7abad681f (add tools up until P)