changeset 1:e14baafb20bd draft

Added Test description, updated a few lines in the help

--- a/cuffquant_wrapper.xml	Mon Aug 04 10:27:05 2014 -0400
+++ b/cuffquant_wrapper.xml	Mon Aug 04 10:43:34 2014 -0400
@@ -48,20 +48,15 @@
 	    #end if
             ## Inputs.
             $gtf_input
-            #for $condition in $conditions:
-                #set samples = ','.join( [ str( $sample.sample ) for $sample in $condition.samples ] )
-                $samples
-            #end for
+            #set samplestring = ','.join( [ str( $sample.sample ) for $sample in $samples ] )
+            $samplestring
     </command>
     <inputs>
         <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript annotation (GFF3 or GTF) file produced by cufflinks, cuffcompare, or other source."/>
 
-        <repeat name="conditions" title="Condition" min="1">
-            <param name="name" title="Condition name" type="text" label="Name"/>
-            <repeat name="samples" title="Replicate" min="1">
-                <param name="sample" label="Add replicate" type="data" format="sam,bam"/>
-            </repeat>
-        </repeat>
+          <repeat name="samples" title="Replicate" min="1">
+               <param name="sample" label="Add replicate" type="data" format="sam,bam"/>
+          </repeat>
 
 
         <param name="multiread_correct" type="boolean" label="Use multi-read correct" help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome." />
@@ -130,7 +125,7 @@
 			</param>
 			<param name="mask_file" type="data" format="gtf,gff3" label="Mask File" help="Ignore all alignment within transcripts in this file" optional="True" />
 			<param name="max_mle_iterations" value="5000" type="integer" label="Max MLE iterations" help="Maximum iterations allowed for Maximal Likelyhood Estimation calculations" />
-			<param name="max_bundle_frags" type="integer" value="500000" label="Maximum number of fragments per locus" help="Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf. Default: 500,000" />
+			<param name="max_bundle_frags" type="integer" value="500000" label="Maximum number of fragments per locus" help="Sets the maximum number of fragments a locus may have before being skipped. Default: 500,000" />
 			
 		    </when>
 		</conditional>
@@ -150,33 +145,17 @@
     <tests>
         <test>
                 <!--
-                    cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam 
+                    cuffquant cuffcompare_out5.gtf cuffdiff_in1.sam,cuffdiff_in2.sam 
                 -->
-                <!-- 
-                    NOTE: as of version 0.0.6 of the wrapper, tests cannot be run because multiple inputs to a repeat
-                    element are not supported.
-                <param name="gtf_input" value="cuffcompare_out5.gtf" ftype="gtf" />
-                <param name="do_groups" value="No" />
-                <param name="aligned_reads1" value="cuffdiff_in1.sam" ftype="sam" />
-                <param name="aligned_reads2" value="cuffdiff_in2.sam" ftype="sam" />
-                <param name="fdr" value="0.05" />
-                <param name="min_alignment_count" value="0" />
+                <param name="gtf_input" value="cuffquant_in.gtf" ftype="gtf" />
+                <param name="sample1" value="cuffquant_in1.sam" ftype="sam" />
+                <param name="sample2" value="cuffquant_in2.sam" ftype="sam" />
+		<param name="length_correction" value="cufflinks effective length correction" />
                 <param name="do_bias_correction" value="No" />
-                <param name="do_normalization" value="No" />
                 <param name="multiread_correct" value="No"/>
                 <param name="sAdditional" value="No"/>
-                <output name="splicing_diff" file="cuffdiff_out9.txt"/>
-                <output name="promoters_diff" file="cuffdiff_out10.txt"/>
-                <output name="cds_diff" file="cuffdiff_out11.txt"/>
-                <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/>
-                <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/>
-                <output name="tss_groups_exp" file="cuffdiff_out3.txt" lines_diff="200"/>
-                <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/>
-                <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="200"/>
-                <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/>
-                <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="200"/>
-                <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="200"/>
-                -->
+		<param name="sAdvanced" value="No" />
+                <output name="out_file" file="cuffquant_out1.cxb"/>
         </test>
     </tests>