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view rapsodyn/rapsodyn_stats.xml @ 15:b65abe3ecda1 draft

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author mcharles
date Wed, 20 Aug 2014 12:17:41 -0400
parents f487491e1091
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<tool id="rapsodyn_stats" name="rapsodyn_stats" version="0.01">
<description>Merge best results from Blast</description>
<command interpreter="perl">
    rapsodyn_stats.pl $input_read1_row_file $input_read2_row_file $input_read1_trimmed_file $input_read2_trimmed_file $input_read1_trimmednoN_file $input_read2_trimmednoN_file $input_sam_row_file $input_sam_filtered_file $input_mpileup_row_file $input_mpileup_filtered_file $input_list_filtered_file $input_blast_filtered_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_read1_trimmednoN_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 TRIMMED noN file from your history"/>
<param name="input_read2_trimmednoN_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 TRIMMED noN 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_row_file"  type="data" format="pileup" label="Select a suitable input MPILEUP file from your history"/>
<param name="input_mpileup_filtered_file"  type="data" format="pileup" label="Select a suitable input MPILEUP FILTERED 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"/>
</inputs>
<outputs>
 <data name="output_file" format="txt" label="STATS"/>
</outputs>


<help>

</help>
</tool>