comparison trinityrnaseq.xml @ 11:2bc2f0d5e4e1 draft

change compute node selection params

10:40f2eee4f2e3

        <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
        <requirement type="package" version="0.1.19">samtools</requirement>
        <requirement type="package" version="1.0.0">bowtie</requirement>
    </requirements>
    <command>
        Trinity.pl --JM $JM --CPU $CPU
        
        ## Inputs.
        #if str($inputs.paired_or_single) == "paired":
            --left $inputs.left_input --right $inputs.right_input
            #if  $inputs.left_input.ext == 'fa':

            #end if
        #end if

        ## Additional parameters.
        #if str($additional_params.use_additional) == "yes":
			--min_kmer_cov $additional_params.min_kmer_cov --max_reads_per_graph $additional_params.max_reads_per_graph --bflyHeapSpaceMax $additional_params.bflyHeapSpaceMax
			#if $additional_params.bfly_opts != 'None':
				--bfly_opts " $additional_params.bfly_opts "
			#end if
        #end if

        | grep 'All commands completed successfully.' > /dev/null
        ## Print the stats to output to provide info on galaxy history item
        && \$TRINITY_HOME/util/TrinityStats.pl trinity_out_dir/Trinity.fasta
    </command>
    <inputs>
        <param name="JM" type="select" label="JM" help="Amount of memory to allocate to Jellyfish for Kmer catalog construction">
            <option value="1G">1G</option>
            <option value="10G">10G</option>
            <option value="50G">50G</option>
            <option value="100G">100G</option>
            <option value="200G">200G</option>
            <option value="500G">500G</option>
        </param>

        <param name="CPU" type="integer" value="2" min="1" label="CPU" help="Number of CPUs to use by Trinity" />


        <conditional name="inputs">
            <param name="paired_or_single" type="select" label="Paired or Single-end data?">
                <option value="paired">Paired</option>
                <option value="single">Single</option>

            </when>
            <when value="yes">            
                <param name="min_kmer_cov" type="integer" value="1" min="1" label="inchworm_min_kmer_cov" help="Minimum kmer coverage required by Inchworm for initial contig construction" />
                <param name="max_reads_per_graph" type="integer" value="20000000" min="10000" label="chrysalis_max_reads_per_graph" help="Maximum number of reads to be anchored within each transcript graph by Chrysalis" />
                <param name="bfly_opts" type="text" value="None" label="bfly_opts" help="Options to pass on to Butterfly" />
                <param name="bflyHeapSpaceMax" type="select" label="bflyHeapSpaceMax" help="Java heap space maximum value for Butterfly">
                    <option value="1G">1G</option>
                    <option value="2G">2G</option>
                    <option value="4G" selected="true">4G</option>
                    <option value="10G">10G</option>
                    <option value="20G">20G</option>
                </param>
               <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/>
            </when>
        </conditional>
    </inputs>
    <stdio>

        <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
    </outputs>
    <tests>

        <test>
            <param name="JM" value="1G"/>
            <param name="CPU" value="1"/>
            <param name="paired_or_single" value="single"/>
            <param name="input" ftype="fastq" value="reads.left.fq"/>
            <param name="library_type" value="None"/>
            <param name="path_reinforcement_distance" value="40"/>
            <param name="use_additional" value="no"/>

                </assert_contents>
            </output>
        </test>

        <test>
            <param name="JM" value="1G"/>
            <param name="CPU" value="1"/>
            <param name="paired_or_single" value="paired"/>
            <param name="left_input" ftype="fastq" value="reads.left.fq"/>
            <param name="right_input" ftype="fastq" value="reads.right.fq"/>
            <param name="library_type" value="None"/>
            <param name="group_pairs_distance" value="500"/>

11:2bc2f0d5e4e1

        <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
        <requirement type="package" version="0.1.19">samtools</requirement>
        <requirement type="package" version="1.0.0">bowtie</requirement>
    </requirements>
    <command>
        Trinity.pl --JM $computenode --CPU \$GALAXY_SLOTS
        
        ## Inputs.
        #if str($inputs.paired_or_single) == "paired":
            --left $inputs.left_input --right $inputs.right_input
            #if  $inputs.left_input.ext == 'fa':

            #end if
        #end if

        ## Additional parameters.
        #if str($additional_params.use_additional) == "yes":
			--min_kmer_cov $additional_params.min_kmer_cov --max_reads_per_graph $additional_params.max_reads_per_graph --bflyHeapSpaceMax $computenode
			#if $additional_params.bfly_opts != 'None':
				--bfly_opts " $additional_params.bfly_opts "
			#end if
        #end if

        | grep 'All commands completed successfully.' > /dev/null
        ## Print the stats to output to provide info on galaxy history item
        && \$TRINITY_HOME/util/TrinityStats.pl trinity_out_dir/Trinity.fasta
    </command>
    <inputs>
      <param name="computenode" type="select" label="Compute node" help="Select the size of node needed">
        <option value="22G">22GB - 8 cores (itasca batch)</option>
        <option value="62G">62GB - 16 cores</option>
        <option value="126G">126GB - 16 cores</option>
        <option value="256G">254GB - 16 cores</option>
      </param>

        <conditional name="inputs">
            <param name="paired_or_single" type="select" label="Paired or Single-end data?">
                <option value="paired">Paired</option>
                <option value="single">Single</option>

            </when>
            <when value="yes">            
                <param name="min_kmer_cov" type="integer" value="1" min="1" label="inchworm_min_kmer_cov" help="Minimum kmer coverage required by Inchworm for initial contig construction" />
                <param name="max_reads_per_graph" type="integer" value="20000000" min="10000" label="chrysalis_max_reads_per_graph" help="Maximum number of reads to be anchored within each transcript graph by Chrysalis" />
                <param name="bfly_opts" type="text" value="None" label="bfly_opts" help="Options to pass on to Butterfly" />
               <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/>
            </when>
        </conditional>
    </inputs>
    <stdio>

        <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
    </outputs>
    <tests>

        <test>
            <param name="paired_or_single" value="single"/>
            <param name="input" ftype="fastq" value="reads.left.fq"/>
            <param name="library_type" value="None"/>
            <param name="path_reinforcement_distance" value="40"/>
            <param name="use_additional" value="no"/>

                </assert_contents>
            </output>
        </test>

        <test>
            <param name="paired_or_single" value="paired"/>
            <param name="left_input" ftype="fastq" value="reads.left.fq"/>
            <param name="right_input" ftype="fastq" value="reads.right.fq"/>
            <param name="library_type" value="None"/>
            <param name="group_pairs_distance" value="500"/>