diff fastqc_report.xml @ 16:1710b0e874f1 draft

fix file name issue

--- a/fastqc_report.xml	Thu Oct 19 00:11:14 2017 -0400
+++ b/fastqc_report.xml	Sat Oct 21 09:25:49 2017 -0400
@@ -1,6 +1,7 @@
 <tool id="fastqc_report" name="Fastqc report" version="2.0.0">
     <description>
-        Implements FastQC analysis and display results in R Markdown html.
+        Evaluate short reads with FastQC software on a single reads file or a paired of untrimmed and trimmed reads
+        files.
     </description>
     <requirements>
         <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
@@ -29,8 +30,12 @@
 
         Rscript '${__tool_directory__}/fastqc_report_render.R'
             -e $echo
-            -r $reads
-            -n $reads.name
+            -r $reads_1
+            -n '$reads_1.name'
+            -R $reads_2
+            -N '$reads_2.name'
+            -c $contaminants
+            -l $limits
 
 		    -o $report
 		    -d $report.files_path
@@ -40,8 +45,23 @@
         ]]>
     </command>
     <inputs>
-        <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads" type="data"
-               label="Short reads data from history"/>
+        <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads_1" type="data" optional="false"
+               label="Short reads before trimming"
+               help="Short reads data from history. This could be reads before trimming."/>
+        <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads_2" type="data"
+               label="Short reads after trimming"
+               help="Short reads data from history. This could be reads after trimming."/>
+        <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list"
+               help="Specifies a non-default file which contains the list of adapter sequences which will be explicitly
+                     searched against the library. The file must contain sets of named adapters
+                     in the form name[tab]sequence.  Lines prefixed with a hash will be ignored."/>
+        <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file"
+               help="Specifies a non-default file which contains a set of criteria
+                    which will be used to determine the warn/error limits for the
+                    various modules.  This file can also be used to selectively
+                    remove some modules from the output all together.  The format
+                    needs to mirror the default limits.txt file found in the
+                    Configuration folder."/>
         <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
                label="Display analysis code in report?"/>
     </inputs>