--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/obisort.xml.orig	Wed Sep 01 07:49:38 2021 +0000
@@ -0,0 +1,133 @@
+<<<<<<< HEAD
+<tool id="obi_sort" name="obisort" version="@TOOL_VERSION@" profile="@PROFILE@">
+    <description>sorts sequence records according to the value of a given attribute</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <command><![CDATA[
+        @GUNZIP_INPUT@
+        obisort
+        --without-progress-bar
+        -k '$key'
+        ${reverse}
+        @INPUT_FORMAT@
+        @OUT_FORMAT@
+        input
+        @GZIP_OUTPUT@
+        > '$output'
+        @GENERATE_GALAXY_JSON@
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" />
+        <param name="key" type="text" label="key"/>
+        <param name="reverse" type="boolean" checked="false" truevalue="-r" falsevalue="" label="sorts in reverse order?" />
+        <expand macro="input_format_options_macro"/>
+        <expand macro="out_format_macro"/>
+    </inputs>
+    <outputs>
+        <data format="auto" name="output"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="output_obiclean_advanced.fasta" />
+            <param name="key" value="count"/>
+            <param name="reverse" value="False"/>
+            <param name="out_format" value="fasta"/>
+            <output name="output" file="output_obisort.fasta" ftype="fasta"/>
+        </test>
+        <test>
+            <param name="input" value="output_obiclean_advanced.fasta" />
+            <param name="key" value="count"/>
+            <param name="reverse" value="True"/>
+            <param name="out_format" value="fastq"/>
+            <output name="output" file="output_obisort.fastq" ftype="fastqsanger"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+obisort sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric.
+
+@OBITOOLS_LINK@
+
+        ]]>
+
+    </help>
+    <expand macro="citation" />
+</tool>
+=======
+<tool id="obi_sort" name="obisort" version="@TOOL_VERSION@">
+    <description>sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric</description>
+    <expand macro="bio_tools"/>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <command>
+
+        <![CDATA[
+            obisort
+            -k '$key'
+            ${reverse}
+            '$input' > '$output'
+        ]]>
+
+    </command>
+
+    <inputs>
+        <param name="input" type="data" format="fastq,fasta,txt,tabular" label="Input sequences file" />
+        <param name="key" type="text" label="key" />
+        <param name="reverse" type="boolean" checked="false" truevalue="-r" falsevalue="" label="sorts in reverse order?" />
+        <param name="out_format" type="select" label="Output data type">
+            <option value="fasta">fasta</option>
+            <option value="fastq">fastq</option>
+        </param>
+
+    </inputs>
+    <outputs>
+        <data format="fastq" name="output" label="output with ${tool.name} on ${on_string}" >
+            <change_format>
+                <when input="out_format" value="fasta" format="fasta" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="output_obiclean_advanced.fasta" />
+            <param name="key" value="count"/>
+            <param name="reverse" value="False"/>
+            <param name="out_format" value="fasta"/>
+            <output name="output" file="output_obisort.fasta" ftype="fasta"/>
+        </test>
+        <test>
+            <param name="input" value="output_obiclean_advanced.fasta" />
+            <param name="key" value="count"/>
+            <param name="reverse" value="True"/>
+            <param name="out_format" value="fastq"/>
+            <output name="output" file="output_obisort.fastq" ftype="fastq"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+obisort sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric.
+
+@OBITOOLS_LINK@
+
+        ]]>
+
+    </help>
+    <expand macro="citation" />
+</tool>
+>>>>>>> 7abad681f (add tools up until P)