comparison sailfish.xml @ 1:06646e81c543 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sailfish commit 326fbf6e8070a792e3bda3256e5465c2d5b1eb71

0:3b4ed0e473dc

        <requirement type="package" version="0.7.6">sailfish</requirement>
    </requirements>
    <macros>
        <xml name="strandedness">
            <param name="strandedness" type="select" label="Specify the strandedness of the reads">
                <option value="U" selected="True">Not stranded</option>
                <option value="SF">read 1 (or single-end read) comes from the forward strand</option>
                <option value="SR">read 1 (or single-end read) comes from the reverse strand</option>
            </param>
        </xml>
    </macros>
    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <regex match="Error:" />
        <regex match="Exception:" />
    </stdio>
    <version_command>sailfish -version</version_command>
    <command>
<![CDATA[

        #end if

        &&

        #if $single_or_paired.single_or_paired_opts == 'single':
            ln -s $single_or_paired.input_singles ./single.$single_or_paired.input_singles.ext &&
        #else:
            ln -s $single_or_paired.input_mate1 ./mate1.$single_or_paired.input_mate1.ext &&
            ln -s $single_or_paired.input_mate2 ./mate2.$single_or_paired.input_mate2.ext &&
        #end if


        #if $geneMap:
            ln -s "$geneMap" ./geneMap.$geneMap.ext &&
        #end if

        sailfish quant
            --index $index_path
            #if $single_or_paired.single_or_paired_opts == 'single':
                --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
                --unmated_reads ./single.$single_or_paired.input_singles.ext
            #else:
                --mates1 ./mate1.$single_or_paired.input_mate1.ext
                --mates2 ./mate2.$single_or_paired.input_mate2.ext
                --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
            #end if
            --output ./ 
            $biasCorrect
            --threads "\${GALAXY_SLOTS:-4}"

    </inputs>
    <outputs>
        <data name="output_quant" format="tabular" from_work_dir="quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
        <data name="output_bias_corrected_quant" format="tabular" from_work_dir="quant_bias_corrected.sf" label="${tool.name} on ${on_string} (Bias corrected Quantification)">
            <filter>bias_correct == '--biasCorrect'</filter>
        </data>
        <data name="output_gene_quant" format="tabular" from_work_dir="quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">
            <filter>geneMap is True</filter>
        </data>
    </outputs>

1:06646e81c543

        <requirement type="package" version="0.7.6">sailfish</requirement>
    </requirements>
    <macros>
        <xml name="strandedness">
            <param name="strandedness" type="select" label="Specify the strandedness of the reads">
                <option value="U" selected="True">Not stranded (U)</option>
                <option value="SF">read 1 (or single-end read) comes from the forward strand (SF)</option>
                <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option>
            </param>
        </xml>
    </macros>
    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <regex match="Error:" />
        <regex match="Exception:" />
        <regex match="Exception :" />
    </stdio>
    <version_command>sailfish -version</version_command>
    <command>
<![CDATA[

        #end if

        &&

        #if $single_or_paired.single_or_paired_opts == 'single':

            #if $single_or_paired.input_singles.ext == 'fasta':
                #set $ext = 'fasta'
            #else:
                #set $ext = 'fastq'
            #end if

            ln -s $single_or_paired.input_singles ./single.$ext &&
        #else:

            #if $single_or_paired.input_mate1.ext == 'fasta':
                #set $ext = 'fasta'
            #else:
                #set $ext = 'fastq'
            #end if

            ln -s $single_or_paired.input_mate1 ./mate1.$ext &&
            ln -s $single_or_paired.input_mate2 ./mate2.$ext &&
        #end if


        #if $geneMap:
            ln -s "$geneMap" ./geneMap.$geneMap.ext &&
        #end if

        sailfish quant
            --index $index_path
            #if $single_or_paired.single_or_paired_opts == 'single':
                --libType ${single_or_paired.strandedness}
                --unmatedReads ./single.$ext
            #else:
                --mates1 ./mate1.$ext
                --mates2 ./mate2.$ext
                --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
            #end if
            --output ./ 
            $biasCorrect
            --threads "\${GALAXY_SLOTS:-4}"

    </inputs>
    <outputs>
        <data name="output_quant" format="tabular" from_work_dir="quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
        <data name="output_bias_corrected_quant" format="tabular" from_work_dir="quant_bias_corrected.sf" label="${tool.name} on ${on_string} (Bias corrected Quantification)">
            <filter>biasCorrect is True</filter>
        </data>
        <data name="output_gene_quant" format="tabular" from_work_dir="quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">
            <filter>geneMap is True</filter>
        </data>
    </outputs>