diff rgFastQC.xml @ 15:2b0c9d9fc6ca draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 35d722c0cafe2a2f2e4e2f73c265ae56ae237997

--- a/rgFastQC.xml	Mon Oct 23 13:26:32 2017 -0400
+++ b/rgFastQC.xml	Fri Nov 24 08:18:41 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="fastqc" name="FastQC" version="0.69">
+<tool id="fastqc" name="FastQC" version="0.70">
     <description>Read Quality reports</description>
     <requirements>
         <requirement type="package" version="0.11.5">fastqc</requirement>
@@ -6,19 +6,45 @@
     <command detect_errors="exit_code"><![CDATA[
         #import re
         #set input_name = re.sub('[^\w\-\s]', '_', str($input_file.element_identifier))
-        python '$__tool_directory__/rgFastQC.py'
-            -i '$input_file'
-            -d '$html_file.files_path'
-            -o '$html_file'
-            -t '$text_file'
-            -f '$input_file.ext'
-            -j '$input_name'
+        
+        #if $input_file.ext.endswith('.gz'):
+            #set input_file_sl = $input_name + '.gz'
+        #elif $input_file.ext.endswith('.bz2'):
+            #set input_file_sl = $input_name + '.bz2'
+        #else
+            #set input_file_sl = $input_name
+        #end if
+
+        #if 'bam' in $input_file.ext:
+            #set format = 'bam'
+        #elif 'sam' in $input_file.ext:
+            #set format = 'sam'
+        #else
+            #set format = 'fastq'
+        #end if
+
+
+        ln -s '${input_file}' '${input_file_sl}' &&
+        mkdir -p '${html_file.files_path}' &&
+        fastqc
+            --outdir '${html_file.files_path}'
+            
             #if $contaminants.dataset and str($contaminants) > ''
-                -c '$contaminants'
+                --contaminants '${contaminants}'
             #end if
+            
             #if $limits.dataset and str($limits) > ''
-                -l '$limits'
+                --limits '${limits}'
             #end if
+            
+            --quiet
+            --extract
+            -f '${format}'
+            '${input_file_sl}'
+
+        && cp '${html_file.files_path}'/*/fastqc_data.txt output.txt
+        && cp '${html_file.files_path}'/*\.html output.html
+
     ]]></command>
     <inputs>
         <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="input_file" type="data"
@@ -29,33 +55,38 @@
                help="a file that specifies which submodules are to be executed (default=all) and also specifies the thresholds for the each submodules warning parameter" />
     </inputs>
     <outputs>
-        <data format="html" name="html_file" label="${tool.name} on ${on_string}: Webpage" />
-        <data format="txt" name="text_file"  label="${tool.name} on ${on_string}: RawData" />
+        <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Webpage" />
+        <data format="txt" name="text_file"  from_work_dir="output.txt" label="${tool.name} on ${on_string}: RawData" />
     </outputs>
     <tests>
         <test>
             <param name="input_file" value="1000gsample.fastq" />
             <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
             <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
-            <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="100"/>
+            <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/>
         </test>
         <test>
             <param name="input_file" value="1000gsample.fastq" />
             <param name="limits" value="fastqc_customlimits.txt" ftype="txt" />
             <output name="html_file" file="fastqc_report2.html" ftype="html" compare="sim_size" delta="4096"/>
-            <output name="text_file" file="fastqc_data2.txt" ftype="txt" compare="sim_size"/>
+            <output name="text_file" file="fastqc_data2.txt" ftype="txt" lines_diff="2"/>
         </test>
         <test>
             <param name="input_file" value="1000gsample.fastq.gz" ftype="fastq.gz" />
             <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
             <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
-            <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="100"/>
+            <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/>
         </test>
         <test>
             <param name="input_file" value="1000gsample.fastq.bz2" ftype="fastq.bz2" />
             <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
             <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
-            <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="100"/>
+            <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/>
+        </test>
+        <test>
+            <param name="input_file" value="hisat_output_1.bam" ftype="bam" />
+            <output name="html_file" file="fastqc_report_hisat.html" ftype="html" lines_diff="100"/>
+            <output name="text_file" file="fastqc_data_hisat.txt" ftype="txt" lines_diff="2"/>
         </test>
     </tests>
     <help>