diff lordec.xml @ 6:a32b531f66a0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"

--- a/lordec.xml	Tue Oct 13 21:38:11 2020 +0000
+++ b/lordec.xml	Thu May 06 12:44:48 2021 +0000
@@ -1,5 +1,4 @@
-<?xml version='1.0' encoding='utf-8'?>
-<tool profile="16.04" id="lordec" name="Lordec" version="0.9+galaxy1">
+<tool id="lordec" name="Lordec" version="0.9+galaxy2" profile="@PROFILE@">
     <description>is a set a programs for correcting sequencing errors in PacBio reads</description>
     <macros>
         <import>macros.xml</import>
@@ -7,21 +6,18 @@
     <requirements>
         <requirement type="package" version="0.9">lordec</requirement>
     </requirements>
-    <command><![CDATA[
-
-        #if str( $program_type_choice.program_type ) == "correct"
+    <command detect_errors="exit_code"><![CDATA[
+        #if str( $program_type_choice.program_type ) == "correct":
             lordec-correct
             @lordec_inputs@
-            #if str( $program_type_choice.advanced_options.advanced_options_selector ) == "advanced"
+            #if str( $program_type_choice.advanced_options.advanced_options_selector ) == "advanced":
                 -t ${program_type_choice.advanced_options.t}
                 -b ${program_type_choice.advanced_options.b}
                 -e ${program_type_choice.advanced_options.e}
             #end if
             -T \${GALAXY_SLOTS:-1}
             -o '${corrected_read_file}'
-
-
-        #else if str( $program_type_choice.program_type ) == "trim"
+        #else if str( $program_type_choice.program_type ) == "trim":
             #if $program_type_choice.split
                 lordec-trim-split
             #else
@@ -29,25 +25,19 @@
             #end if
             -i '${program_type_choice.i}'
             -o '${trimmed_reads_file}'
-
         #else
             lordec-stat
             @lordec_inputs@
             -S '${stat_file}'
         #end if
-
-
     ]]></command>
-
     <inputs>
-
         <conditional name="program_type_choice">
             <param name="program_type" type="select" label="Choose Lordec program">
                 <option value="correct">Lordec Correct</option>
                 <option value="trim">Lordec Trim</option>
                 <option value="stats">Lordec Statistics</option>
             </param>
-
             <when value="correct">
                 <expand macro="lordec_inputs" />
                 <conditional name="advanced_options">
@@ -63,20 +53,15 @@
                     </when>
                 </conditional>
             </when>
-
             <when value="trim">
-                <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" />
+                <param argument="-i" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Long read FASTA/Q file" help="PacBio reads files" />
                 <param name="split" type="boolean" label="Use the split option" help="Trim all weak regions and split the reads on inner weak regions" />
             </when>
-
             <when value="stats">
                 <expand macro="lordec_inputs" />
             </when>
-
         </conditional>
-
     </inputs>
-
     <outputs>
         <data format="fasta" name="corrected_read_file" label="Corrected long reads with ${tool.name} on ${on_string}" >
             <filter>program_type_choice['program_type'] == 'correct'</filter>
@@ -88,13 +73,12 @@
             <filter>program_type_choice['program_type'] == 'stats'</filter>
         </data>
     </outputs>
-
     <tests>
         <test>
             <conditional name="program_type_choice">
                 <param name="program_type" value="correct" />
-                <param name="inputs" value="lordec/ill-test-5K-1.fa,lordec/ill-test-5K-2.fa" />
-                <param name="i" value="lordec/coli-pacbio-test-mini.fa" />
+                <param name="inputs" value="lordec/ill-test-5K-1.fa.gz,lordec/ill-test-5K-2.fa.gz" ftype="fasta.gz"/>
+                <param name="i" value="lordec/coli-pacbio-test-mini.fa.gz" />
                 <param name="k" value="31" />
             </conditional>
             <output name="corrected_read_file" file="lordec/corrected_reads.fa"/>
@@ -102,15 +86,15 @@
         <test>
             <conditional name="program_type_choice">
                 <param name="program_type" value="trim" />
-                <param name="i" value="lordec/corrected_reads.fa" />
+                <param name="i" value="lordec/corrected_reads.fa" ftype="fasta"/>
             </conditional>
             <output name="trimmed_reads_file" file="lordec/trimmed_reads.fa"/>
         </test>
         <test>
             <conditional name="program_type_choice">
                 <param name="program_type" value="stats" />
-                <param name="inputs" value="lordec/ill-test-5K-1.fa,lordec/ill-test-5K-2.fa" />
-                <param name="i" value="lordec/coli-pacbio-test-mini.fa" />
+                <param name="inputs" value="lordec/ill-test-5K-1.fa.gz,lordec/ill-test-5K-2.fa.gz" />
+                <param name="i" value="lordec/coli-pacbio-test-mini.fa.gz" />
             </conditional>
             <output name="stat_file" file="lordec/stat_file.txt" compare="sim_size" delta="10"/>
         </test>