diff scpipe.xml @ 1:4ec6717872b1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit ffcc4ba8dcf01fd19bee6d946f9789bcf4ed680a
author iuc
date Fri, 17 Aug 2018 08:22:49 -0400
parents 32e1bfc6b7b2
children 5c4bca9dd4a2
line wrap: on
line diff
--- a/scpipe.xml	Wed Aug 15 13:54:40 2018 -0400
+++ b/scpipe.xml	Fri Aug 17 08:22:49 2018 -0400
@@ -28,7 +28,7 @@
     #set $fasta_name = re.sub('[^\w\-\s]', '_', str($ref_fasta.ref_fa_hist.element_identifier))
     ln -s '$ref_fasta.ref_fa_hist' '$fasta_name' &&
 #else:
-    #set $fasta_name = re.sub('[^\w\-\s]', '_', str($ref_fasta.ref_fa_builtin.element_identifier))
+    #set $fasta_name = os.path.basename(str($ref_fasta.ref_fa_builtin.fields.path))
     ln -s '$ref_fasta.ref_fa_builtin.fields.path' '$fasta_name' &&
 #end if
 
@@ -156,12 +156,12 @@
             help="Output all the data used by R to construct the tables and plots, can be loaded into R. Default: No">
         </param>
         <section name="adv" title="Advanced Options">
-            <param argument="--rmlow" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with N in barcode or UMI. Default: Yes" />
-            <param argument="--rmN" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with low quality. Default: Yes" />
-            <param argument="--minq" type="integer" min="0" value="20" label="Minimum read quality. Default: 20" />
-            <param argument="--numbq" type="integer" min="0" value="2" label="Maximum number of bases below minq. Default: 2" />
-            <param argument="--stnd" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Perform strand-specific mapping. Default: Yes" />
-            <param argument="--max_mis" type="integer" min="0" value="1" label="Maximum mismatch allowed in barcode. Default: 1" />
+            <param argument="--rmlow" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with N in barcode or UMI" help="Default: Yes" />
+            <param argument="--rmN" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with low quality" help="Default: Yes" />
+            <param argument="--minq" type="integer" min="0" value="20" label="Minimum read quality" help="Default: 20" />
+            <param argument="--numbq" type="integer" min="0" value="2" label="Maximum number of bases below minq" help="Default: 2" />
+            <param argument="--stnd" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Perform strand-specific mapping" help="Default: Yes" />
+            <param argument="--max_mis" type="integer" min="0" value="1" label="Maximum mismatch allowed in barcode" help="Default: 1" />
             <param argument="--UMI_cor" type="integer" min="0" value="1" label="Correct UMI sequence error" help="0 means no correction, 1 means simple correction and merge UMI with distance 1. Default: 1" />
             <param argument="--gene_fl" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Remove low abundant genes" help="Low abundant is defined as only one copy of one UMI for this gene. Default: No" />
             <param argument="--max_reads" type="integer" min="0" value="1000000" label="Maximum reads processed" help="Maximum reads processed if detecting barcodes. Default: 1,000,000" />
@@ -206,6 +206,23 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Ensure built-in fasta works -->
+        <test>
+            <param name="fasta_source" value="cached"/>
+            <param name="exons" ftype="gff3" value="mm10_MT19.gff3.gz"/>
+            <param name="paired_format_selector" value="paired" />
+            <param name="in1" ftype="fastqsanger.gz" dbkey="mm10" value="CB51_MT19_R1.gz"/>
+            <param name="in2" ftype="fastqsanger.gz" dbkey="mm10" value="CB51_MT19_R2.gz"/>
+            <param name="us" value="-1"/>
+            <param name="max_reads" value="5000000"/>
+            <param name="min_count" value="100"/>
+            <param name="report" value="False" />
+            <output name="out_matrix" >
+                <assert_contents>
+                    <has_text text="ENSMUSG00000064351" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 .. class:: infomark