diff biotradis_remove_tags.xml @ 7:09c1f97a5bcc draft

"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 1c12becfd708c0635632ab92620a846764ec4559-dirty"

--- a/biotradis_remove_tags.xml	Wed Oct 23 10:40:28 2019 -0400
+++ b/biotradis_remove_tags.xml	Fri Dec 06 10:11:20 2019 -0500
@@ -6,18 +6,18 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
     
-    remove_tags -f $input_bam -t $tag -m $mismatches -o removed -v > $log
+    remove_tradis_tags -f $input_bam -t $tag -m $mismatches -o removed -v > $log
 
-    ]]></command>
+    ]]>    </command>
     <inputs>
-         <param name="input_fastq" type="data" format="fastq" label="Fastq file" help="" />
-         <param name="tag" type="text" label="Tags to remove" help="" />
-         <param name="mismatches" type="integer" value ="0" label="Number of mismatches to allow when matching tag" help="(optional. default = 0)" />
+        <param name="input_fastq" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Fastq file"/>
+        <param name="tag" type="text" label="Tags to remove" />
+        <param name="mismatches" type="integer" min="0" value ="0" label="Number of mismatches to allow when matching tag" />
     </inputs>
 
     <outputs>
-       <data name="log" format="txt" label="${tool.name} on ${on_string}: Log"/>
-       <data name="filtered_tags" format="fastqsanger" label="${tool.name} on ${on_string}" from_work_dir="removed.rmtag.fatsq" />
+        <data name="log" format="txt" label="${tool.name} on ${on_string}: Log"/>
+        <data name="filtered_tags" format="fastqsanger" label="${tool.name} on ${on_string}" from_work_dir="removed.rmtag.fatsq" />
     </outputs>
 
     <tests>
@@ -31,6 +31,7 @@
         Options:
         -b  : bam file with tradis tags
         -v  : verbose debugging output
-    ]]></help>
+    ]]>    </help>
+    <expand macro="citations" />
 
 </tool>