Mercurial > repos > mcharles > rapsosnp

diff rapsodyn/rapsosnp_stats4x.xml @ 2:761fecc07fa9 draft

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author mcharles
date Thu, 11 Sep 2014 03:10:47 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/rapsosnp_stats4x.xml	Thu Sep 11 03:10:47 2014 -0400
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+<tool id="rapsosnp_stats4x" name="rapsosnp_stats4x" version="0.01">
+<description>Stats for rapsosnp workflow</description>
+<command interpreter="perl">
+    rapsosnp_stats4x.pl $input_read1_row_file $input_read2_row_file $input_read1_part1_trimmed_file $input_read1_part2_trimmed_file $input_read1_part3_trimmed_file $input_read1_part4_trimmed_file $input_read2_part1_trimmed_file $input_read2_part2_trimmed_file $input_read2_part3_trimmed_file $input_read2_part4_trimmed_file $input_sam_row_part1_file $input_sam_row_part2_file $input_sam_row_part3_file $input_sam_row_part4_file $input_sam_filtered_part1_file $input_sam_filtered_part2_file $input_sam_filtered_part3_file $input_sam_filtered_part4_file $input_mpileup_variant_file $input_list_filtered_file $input_blast_filtered_part1_file $input_blast_filtered_part2_file $input_blast_filtered_part3_file $input_blast_filtered_part4_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_part1_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 PART1 TRIMMED file from your history"/>
+<param name="input_read1_part2_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 PART2 TRIMMED file from your history"/>
+<param name="input_read1_part3_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 PART3 TRIMMED file from your history"/>
+<param name="input_read1_part4_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 PART4 TRIMMED file from your history"/>
+<param name="input_read2_part1_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 PART1 TRIMMED file from your history"/>
+<param name="input_read2_part2_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 PART2 TRIMMED file from your history"/>
+<param name="input_read2_part3_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 PART3 TRIMMED file from your history"/>
+<param name="input_read2_part4_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 PART4 TRIMMED file from your history"/>
+
+<param name="input_sam_row_part1_file"  type="data" format="sam" label="Select a suitable input SAM PART1 file from your history"/>
+<param name="input_sam_row_part2_file"  type="data" format="sam" label="Select a suitable input SAM PART2 file from your history"/>
+<param name="input_sam_row_part3_file"  type="data" format="sam" label="Select a suitable input SAM PART3 file from your history"/>
+<param name="input_sam_row_part4_file"  type="data" format="sam" label="Select a suitable input SAM PART4 file from your history"/>
+<param name="input_sam_filtered_part1_file"  type="data" format="sam" label="Select a suitable input SAM PART1 FILTERED file from your history"/>
+<param name="input_sam_filtered_part2_file"  type="data" format="sam" label="Select a suitable input SAM PART2 FILTERED file from your history"/>
+<param name="input_sam_filtered_part3_file"  type="data" format="sam" label="Select a suitable input SAM PART3 FILTERED file from your history"/>
+<param name="input_sam_filtered_part4_file"  type="data" format="sam" label="Select a suitable input SAM PART4 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_part1_file"  type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART1 file from your history"/>
+<param name="input_blast_filtered_part2_file"  type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART2 file from your history"/>
+<param name="input_blast_filtered_part3_file"  type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART3 file from your history"/>
+<param name="input_blast_filtered_part4_file"  type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART4 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>