diff obisort.xml @ 3:e614dcabd870 draft

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

--- a/obisort.xml	Thu Nov 28 15:51:52 2019 -0500
+++ b/obisort.xml	Mon May 10 19:34:04 2021 +0000
@@ -1,67 +1,62 @@
-<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>
-    <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 ${on_string}" >
-            <change_format>
-                <when input="out_format" value="fasta" format="fasta" />
-            </change_format>
-        </data>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input" value="output_obiclean_advanced.fasta" />
-            <param name="key" value="count"/>
-            <param name="reverse" value="False"/>
-            <param name="out_format" value="fasta"/>
-            <output name="output" file="output_obisort.fasta" ftype="fasta"/>
-        </test>
-        <test>
-            <param name="input" value="output_obiclean_advanced.fasta" />
-            <param name="key" value="count"/>
-            <param name="reverse" value="True"/>
-            <param name="out_format" value="fastq"/>
-            <output name="output" file="output_obisort.fastq" ftype="fastq"/>
-        </test>
-    </tests>
-    <help><![CDATA[
-
-.. class:: infomark
-
-**What it does**
-
-obisort sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric.
-
-@OBITOOLS_LINK@
-
-        ]]>
-
-    </help>
-    <expand macro="citation" />
-</tool>
+<tool id="obi_sort" name="obisort" version="@TOOL_VERSION@" profile="@PROFILE@">
+    <description>sorts sequence records according to the value of a given attribute</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <command><![CDATA[
+        @GUNZIP_INPUT@
+        obisort
+        --without-progress-bar
+        -k '$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>