Mercurial > repos > mcharles > rapsosnp

diff rapsodyn/rapsosnp_stats.xml @ 1:7f36bd129321 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author mcharles
date Wed, 10 Sep 2014 10:24:01 -0400
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/rapsosnp_stats.xml	Wed Sep 10 10:24:01 2014 -0400
@@ -0,0 +1,26 @@
+<tool id="rapsosnp_stats" name="rapsosnp_stats" version="0.01">
+<description>Merge best results from Blast</description>
+<command interpreter="perl">
+    rapsosnp_stats.pl $input_read1_row_file $input_read2_row_file $input_read1_trimmed_file $input_read2_trimmed_file $input_sam_row_file $input_sam_filtered_file $input_mpileup_variant_file $input_list_filtered_file $input_blast_filtered_file $input_snp_selected_file  > $output_file 
+</command>
+<inputs>
+<param name="input_read1_row_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 ROW file from your history"/>
+<param name="input_read2_row_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 ROW file from your history"/>
+<param name="input_read1_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 TRIMMED file from your history"/>
+<param name="input_read2_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 TRIMMED file from your history"/>
+<param name="input_sam_row_file"  type="data" format="sam" label="Select a suitable input SAM file from your history"/>
+<param name="input_sam_filtered_file"  type="data" format="sam" label="Select a suitable input SAM FILTERED file from your history"/>
+<param name="input_mpileup_variant_file"  type="data" format="pileup" label="Select a suitable input MPILEUP VARIANT file from your history"/>
+<param name="input_list_filtered_file"  type="data" format="pileup" label="Select a suitable input LIST FILTERED file from your history"/>
+<param name="input_blast_filtered_file"  type="data" format="pileup" label="Select a suitable input BLAST FILTERED file from your history"/>
+<param name="input_snp_selected_file"  type="data" format="pileup" label="Select a suitable input SNP SELECTED file from your history"/>
+</inputs>
+<outputs>
+ <data name="output_file" format="txt" label="STATS"/>
+</outputs>
+
+
+<help>
+
+</help>
+</tool>