diff paired.xml @ 0:40c86e14b674 draft

Uploaded first version of tagdust

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/paired.xml	Mon May 09 04:08:01 2016 -0400
@@ -0,0 +1,95 @@
+<tool id="tagdust_paired_runner_2_31" name="Tagdust paired end runner" version="0.2">
+    <description>Runs tagdust in paired end mode</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"></expand>
+    <expand macro="stdio"></expand>
+    <expand macro="version_command"></expand>
+    <command >
+        @cat-archiecture@
+        cp $read1_file read1.fastq ;
+        cp $read2_file read2.fastq ;
+        @tagdust-call-minus-files@
+            read1.fastq read2.fastq ;
+        @ls_and_barcode@
+    </command>
+    <inputs>
+        <param name="read1_file" type="data" format="fastq,fastqsanger" label="Read 1 Fastq file to process" />
+        <param name="read2_file" type="data" format="fastq,fastqsanger" label="Read 2 Fastq file to process" />
+        <expand macro="reference_source"/>
+        <expand macro="architecture"/>
+        <expand macro="include_barcode_file"/>
+        <expand macro="architecture"></expand>
+    </inputs>
+    <outputs>
+        <data format="txt" name="logfile" label="Tagdust log on ${on_string}." from_work_dir="output/data_logfile.txt"/>
+        <data format_source="read1_file" name="extracted1" label="Tagdust extracted Read1 from ${on_string}." from_work_dir="output/data_READ1.fq"/>
+        <data format_source="read1_file"  name="unextracted1" label="Tagdust un-extracted Read1 from ${on_string}." from_work_dir="output/data_un_READ1.fq"/>
+        <data format_source="read2_file"  name="extracted2" label="Tagdust extracted Read2 from ${on_string}." from_work_dir="output/data_READ2.fq"/>
+        <data format_source="read2_file"  name="unextracted2" label="Tagdust un-extracted Read2 from ${on_string}." from_work_dir="output/data_un_READ2.fq"/>
+        <expand macro="output_barcode"/>
+    </outputs>
+    <tests>
+        <!-- Large dataset in github but not toolshed -->
+        <test>
+            <param name="read1_file" value="C75_S29_R1_001_extracted.fastq" ftype="fastq" /> 
+            <param name="read2_file" value="C75_S29_R2_001_extracted.fastq" ftype="fastq" /> 
+            <param name="architecture" value="R:N" /> 
+            <param name="reference_source|reference_source_selector" value="history"/>
+            <param name="reference_source|ref_file" value="ercc_and_TPA_mouse_rRNA.fa" ftype="fasta"/>
+            <output name="logfile" >
+                <assert_contents>
+                    <has_text text="Determining threshold for read0." />
+                 </assert_contents>
+            </output>
+            <output name="extracted1" file="C75_S29__READ1.fq" compare="sim_size" delta="10000"/>
+            <output name="unextracted1" file="C75_S29__un_READ1.fq"  compare="sim_size" delta="10000"/>
+            <output name="extracted2" file="C75_S29__READ2.fq" compare="sim_size" delta="10000"/>
+            <output name="unextracted2" file="C75_S29__un_READ2.fq"  compare="sim_size" delta="10000"/>
+        </test>
+        <test>
+            <param name="read1_file" value="read1_extracted.fastq" ftype="fastqsanger" /> 
+            <param name="read2_file" value="read2_extracted.fastq" ftype="fastqsanger" /> 
+            <param name="architecture" value="test_R:N" /> 
+            <param name="reference_source|reference_source_selector" value="history"/>
+            <param name="reference_source|ref_file" value="ercc_and_TPA_mouse_rRNA.fa" ftype="fasta"/>
+            <output name="logfile" >
+                <assert_contents>
+                    <has_text text="Determining threshold for read0." />
+                 </assert_contents>
+            </output>
+            <output name="extracted1" file="paired_READ1.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/>
+            <output name="unextracted1" file="paired_un_READ1.fq"  ftype="fastqsanger" compare="sim_size" delta="1000"/>
+            <output name="extracted2" file="paired_READ2.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/>
+            <output name="unextracted2" file="paired_un_READ2.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/>
+        </test>
+        <test>
+            <param name="read1_file" value="read1_extracted.fastq" ftype="fastq" /> 
+            <param name="read2_file" value="read2_extracted.fastq" ftype="fastq" /> 
+            <param name="architecture" value="test_R:N" /> 
+            <param name="reference_source|reference_source_selector" value="cached"/>
+            <param name="ref_path" value="test_ercc_and_TPA_mouse_RNA"/>
+            <output name="logfile" >
+                <assert_contents>
+                    <has_text text="Determining threshold for read0." />
+                 </assert_contents>
+            </output>
+            <output name="extracted1" file="paired_READ1.fq" compare="sim_size" delta="1000"/>
+            <output name="unextracted1" file="paired_un_READ1.fq"  compare="sim_size" delta="1000"/>
+            <output name="extracted2" file="paired_READ2.fq" compare="sim_size" delta="1000"/>
+            <output name="unextracted2" file="paired_un_READ2.fq"  compare="sim_size" delta="1000"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+This tool runs Tagdust2 in paired end mode.
+
+]]>
+@tool-documentation@
+
+@tagdust-documentation@
+
+    </help> 
+    <expand macro="citations"></expand>
+</tool>