changeset 7:904c91ea4d71 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 90d5287f4b11aaa9103a4a2917ca37ab193c5ccf

--- a/trim_galore.xml	Fri Mar 18 07:58:11 2016 -0400
+++ b/trim_galore.xml	Tue Mar 29 12:09:21 2016 -0400
@@ -24,7 +24,6 @@
             </conditional>
         </macro>
         <macro name="paired_adapter_trimming">
-
             <expand macro="adapter_trimming">
                 <param name="adapter2" type="text" optional="True" value="" label="Adapter sequence to be trimmed off read 2">
                     <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
@@ -53,7 +52,6 @@
     </version_command>
     <command>
 <![CDATA[
-
         ## trim_galore removes .fastq and .fq file extensions of input files.
         ## This is essential if Galaxy provides links to files (with real extensions)
         ## but that behaviour is causing an inconsistency in output filenaming.
@@ -140,7 +138,6 @@
             $singlePaired.trimming.trimming_select
         #end if
 
-
         #if $singlePaired.three_prime_clip_R1:
             --three_prime_clip_R1 $singlePaired.three_prime_clip_R1
         #end if
@@ -208,7 +205,6 @@
             &&
             cat ./*_trimming_report.txt > $report_file;
         #end if
-
 ]]>
     </command>
     <inputs>
@@ -222,7 +218,6 @@
             <when value="single">
                 <param name="input_singles" type="data" format="fastqsanger" label="Reads in FASTQ format" />
                 <expand macro="adapter_trimming"/>
-
                 <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end">
                     <help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
                         This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
@@ -240,7 +235,6 @@
                 <expand macro="paired_adapter_trimming" />
             </when>
         </conditional>
-
         <conditional name="params">
             <param name="settingsType" type="select" label="Trim Galore! advanced settings" help="You can use the default settings or set custom values for any of Trim Galore!'s parameters.">
               <option value="default">Use defaults</option>
@@ -257,7 +251,6 @@
 
                 <param name="clip_R1" type="integer" optional="True" min="0" label="Instructs Trim Galore! to remove INT bp from the 5' end of read 1" />
                 <param name="clip_R2" type="integer" optional="True" min="0" label="Instructs Trim Galore! to remove INT bp from the 5' end of read 2" />
-
                 <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Generate a report file" help="" />
 
                 <conditional name="retain_unpaired">
@@ -272,7 +265,6 @@
                         <param name="length_2" type="integer" value="35" label="Unpaired single-end read length cutoff needed for read 2 to be written" />
                     </when>  <!-- output -->
                 </conditional>  <!-- retain_unpaired -->
-
             </when>  <!-- full -->
         </conditional>  <!-- params -->
 
@@ -296,13 +288,11 @@
         <data format="fastqsanger" name="trimmed_reads_single" from_work_dir="input_singles_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads">
             <filter>singlePaired['sPaired'] == "single"</filter>
         </data>
-
         <collection name="trimmed_reads_paired_collection" type="paired" label="${tool.name} on ${on_string}: paired reads">
             <data name="forward" format="fastqsanger" from_work_dir="input_mate1_val_1.fq" />
             <data name="reverse" format="fastqsanger" from_work_dir="input_mate2_val_2.fq" />
             <filter>singlePaired['sPaired'] == "paired_collection"</filter>
         </collection>
-
         <collection name="trimmed_reads_unpaired_collection" type="paired" label="${tool.name} on ${on_string}: unpaired reads">
             <data name="forward" format="fastqsanger" from_work_dir="input_mate1_unpaired_1.fq" />
             <data name="reverse" format="fastqsanger" from_work_dir="input_mate2_unpaired_2.fq" />
@@ -310,24 +300,20 @@
             <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
             <filter>singlePaired['sPaired'] == "paired_collection"</filter>
         </collection>
-
         <data format="fastqsanger" name="trimmed_reads_pair1" from_work_dir="input_mate1_val_1.fq"
             label="${tool.name} on ${on_string}: trimmed reads pair 1">
             <filter>singlePaired['sPaired'] == "paired"</filter>
         </data>
-
         <data format="fastqsanger" name="trimmed_reads_pair2" from_work_dir="input_mate2_val_2.fq"
             label="${tool.name} on ${on_string}: trimmed reads pair 2">
             <filter>singlePaired['sPaired'] == "paired"</filter>
         </data>
-
         <data format="fastqsanger" name="unpaired_reads_1" from_work_dir="input_mate1_unpaired_1.fq"
             label="${tool.name} on ${on_string}: unpaired reads (1)">
             <filter>params['settingsType'] == "custom"</filter>
             <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
             <filter>singlePaired['sPaired'] == "paired"</filter>
         </data>
-
         <data format="fastqsanger" name="unpaired_reads_2" from_work_dir="input_mate2_unpaired_2.fq"
             label="${tool.name} on ${on_string}: unpaired reads (2)">
             <filter>params['settingsType'] == "custom"</filter>
@@ -338,7 +324,6 @@
             <filter>params['settingsType'] == "custom"</filter>
             <filter>params['report'] == True</filter>
         </data>
-
     </outputs>
     <tests>
         <test>