comparison align_cluster.xml @ 2:40371e8b6ee2 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 6f9cc1c762abc9a45af9c459bd2603426148a369-dirty"

1:953353eacec2

          </param>
          <when value="no" />
          <when value="yes" >
              <param format="fasta" name="transcript_loci_fasta" type="data" label="Loci reference sequence"
                help="Sequence of reference species (human) for the genomic loci (precursor mRNA/lncRNA) to locate the clusters" />
              <param name='transcript_loci_bed' type="text" value="chr1 0 100000 gene 0 +" 
                help="bed entry string of the reference transcript loci for bed/ucsc-track output. 'chrom start end name score strand' white-space separated.">
                <validator type="regex" message="one-line bed string must have at least 6 entries as BED6 format (chrom start end name 0 strand) 
                (space and tab allowed)">^\S+\s+[0-9]+\s+[0-9]+\s+\S+\s+\S+\s+[-+]\s*$</validator> 
              </param>
              <param name='genome_version' value="hg38" type="text" label="reference genome assembly"
                help="ucsc reference genome assembly version used in the input MAF alignments (e.g. hg38, hg19, mm10). To identify the reference in clusters">
                  <validator type="regex" message="ucsc genome assembly version has an alphabet prefix and a number suffix">^[a-zA-Z]+[0-9]+$</validator> 
              </param>
          </when>
      </conditional> 

2:40371e8b6ee2

          </param>
          <when value="no" />
          <when value="yes" >
              <param format="fasta" name="transcript_loci_fasta" type="data" label="Loci reference sequence"
                help="Sequence of reference species (human) for the genomic loci (precursor mRNA/lncRNA) to locate the clusters" />
              <param name='transcript_loci_bed' type="txt" value="chr1 0 100000 gene 0 +" 
                help="bed entry string of the reference transcript loci for bed/ucsc-track output. 'chrom start end name score strand' white-space separated.">
                <validator type="regex" message="one-line bed string must have at least 6 entries as BED6 format (chrom start end name 0 strand) 
                (space and tab allowed)">^\S+\s+[0-9]+\s+[0-9]+\s+\S+\s+\S+\s+[-+]\s*$</validator> 
              </param>
              <param name='genome_version' value="hg38" type="txt" label="reference genome assembly"
                help="ucsc reference genome assembly version used in the input MAF alignments (e.g. hg38, hg19, mm10). To identify the reference in clusters">
                  <validator type="regex" message="ucsc genome assembly version has an alphabet prefix and a number suffix">^[a-zA-Z]+[0-9]+$</validator> 
              </param>
          </when>
      </conditional>