diff presto_pairseq.xml @ 3:49e7407445c3 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit d52e3c9c53dd358e14e65a3a083e7d5c102f8697"

--- a/presto_pairseq.xml	Fri Jul 02 15:31:14 2021 +0000
+++ b/presto_pairseq.xml	Sat Sep 25 18:34:52 2021 +0000
@@ -1,12 +1,12 @@
-<tool id="presto_pairseq" name="pRESTO PairSeq" version="@TOOL_VERSION@">
+<tool id="presto_pairseq" name="pRESTO PairSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Sorts and matches sequence records with matching coordinates across files</description>
-    
+    <expand macro="bio_tools"/>
     <macros>
         <import>presto_macros.xml</import>
-    </macros>
-    
-    <expand macro="requirements"/>
-    
+	</macros>
+
+	<expand macro="requirements"/>
+
     <version_command>PairSeq.py --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$r1_in' r1.fastq &&
@@ -21,6 +21,7 @@
           #if $r2_annotations
           --2f $r2_annotations
           #end if
+		  $failed
           --outdir=.
           --outname=tmp
     ]]></command>
@@ -34,14 +35,21 @@
             <expand macro="text-regex-validator"/>
         </param>
         <expand macro="presto-coord-param"/>
+        <param argument="--failed" type="boolean" checked="false" truevalue="--failed" falsevalue="" label="Failed reads fastq output" />
     </inputs>
     <outputs>
         <data name="r1_out" format="fastq" from_work_dir="tmp-1_pair-pass.fastq"/>
         <data name="r2_out" format="fastq" from_work_dir="tmp-2_pair-pass.fastq"/>
+        <!-- only give these 2 outputs if input failed_fastq=True-->
+        <data name="r1_fail_out" format="fastq" from_work_dir="tmp-1_pair-fail.fastq">
+            <filter>failed</filter>
+        </data>
+        <data name="r2_fail_out" format="fastq" from_work_dir="tmp-2_pair-fail.fastq">
+            <filter>failed</filter>
+        </data>
     </outputs>
-    
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="r1_in" value="presto_pairseq_test1_r1_in.fastq"/>
             <param name="r2_in" value="presto_pairseq_test1_r2_in.fastq"/>
             <param name="r2_annotations" value="BARCODE"/>
@@ -49,8 +57,26 @@
             <output name="r1_out" file="presto_pairseq_test1_r1_out.fastq" sort="true"/>
             <output name="r2_out" file="presto_pairseq_test1_r2_out.fastq" sort="true"/>
         </test>
+        <test expect_num_outputs="4">
+            <param name="r1_in" value="presto_pairseq_test1_r1_in.fastq"/>
+            <param name="r2_in" value="presto_pairseq_test1_r2_in.fastq"/>
+            <param name="r2_annotations" value="BARCODE"/>
+            <param name="coord" value="illumina"/>
+            <param name="failed" value="true"/>
+            <output name="r1_out" file="presto_pairseq_test1_r1_out.fastq" sort="true"/>
+            <output name="r2_out" file="presto_pairseq_test1_r2_out.fastq" sort="true"/>
+            <output name="r1_fail_out">
+                <assert_contents>
+                    <has_text text="@"/>
+                </assert_contents>
+            </output>
+            <output name="r2_fail_out">
+                <assert_contents>
+                    <has_text text="@"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
-    
     <help><![CDATA[
 Sorts and matches sequence records with matching coordinates across files.