# HG changeset patch
# User iuc
# Date 1533732566 14400
# Node ID 7c82cb2a90c4a5653730a06fb747d1383f69f6f3
# Parent  e0b44bf2543ee960fcfb4fc69b8af224052f27eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984

diff -r e0b44bf2543e -r 7c82cb2a90c4 fastp.xml
--- a/fastp.xml	Sun Aug 05 18:02:58 2018 -0400
+++ b/fastp.xml	Wed Aug 08 08:49:26 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="fastp" name="fastp" version="@WRAPPER_VERSION@.0">
+<tool id="fastp" name="fastp" version="@WRAPPER_VERSION@.1">
     <description>- fast all-in-one preprocessing for FASTQ files</description>
     <macros>
         <import>macros.xml</import>
@@ -8,44 +8,42 @@
     </requirements>
     <version_command>fastp -v</version_command>
     <command detect_errors="exit_code"><![CDATA[
+#import re
+
 ## Link input files
 
 #if $in1.is_of_type('fastq.gz')
-    #set ext = 'fastq.gz'
+    #set ext = '.fastq.gz'
 #else
-    #set ext = 'fastq'
+    #set ext = '.fastq'
 #end if
 
-ln -s '$in1' input1.$ext &&
+#set $in1_name = re.sub('[^\w\-\s]', '_', str($in1.element_identifier)) + $ext
+ln -s '$in1' $in1_name &&
 
 #if str($single_paired.single_paired_selector) == 'paired':
-    ln -s '$in2' input2.$ext &&
+    #set $in2_name = re.sub('[^\w\-\s]', '_', str($in2.element_identifier)) + $ext
+    ln -s '$in2' $in2_name &&
 #end if
 
 
-## Set filename for output report
-
-#import re
-#set $filename = re.sub('[^\w\-\s]', '_', str($in1.element_identifier))
-
-
 ## Run fastp
 
 fastp
 
 --thread \${GALAXY_SLOTS:-1}
---report_title 'fastp report for $filename'
+--report_title 'fastp report for $in1_name'
 
 #if $in1.is_of_type('fastqillumina', 'fastqsolexa', 'fastqillumina.gz', 'fastqsolexa.gz'):
     --phred64
 #end if
 
--i input1.$ext
--o first.$ext
+-i $in1_name
+-o first${ext}
 
 #if str($single_paired.single_paired_selector) == 'paired':
-    -I input2.$ext
-    -O second.$ext
+    -I $in2_name
+    -O second${ext}
 #end if
 
 
@@ -184,10 +182,10 @@
 
 &&
 
-mv first.$ext '${out1}'
+mv first${ext} '${out1}'
 #if str($single_paired.single_paired_selector) == 'paired':
     &&
-    mv second.$ext '${out2}'
+    mv second${ext} '${out2}'
 #end if
 ]]></command>
     <inputs>
@@ -309,7 +307,7 @@
 
         <section name="output_options" title="Output Options" expanded="False">
             <param name="report_html" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Output HTML report" help="fastp provides a QC report for the data Before and After filtering within a single HTML page, which enables comparison of the quality statistics changed by the preprocessing step directly"/>
-            <param name="report_json" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output JSON report" help="The JSON report contains all the data visualized in the HTML report. The format of the JSON report is manually optimized to be easily readable by humans"/>
+            <param name="report_json" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output JSON report" help="The JSON report contains all the data visualized in the HTML report. The format of the JSON report is manually optimized to be easily readable by humans and is compatible with MultiQC"/>
         </section>
     </inputs>
 
@@ -469,7 +467,7 @@
 Optionally, under **Output Options** you can choose to output
 
     * HTML report (default is Yes)
-    * JSON report
+    * JSON report (compatible with MultiQC)
 
 .. _fastp: https://github.com/OpenGene/fastp