comparison tetyper.xml @ 1:36093854bfc7 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"

0:8bc80c2a15b3

<tool id="tetyper" name="TETyper" version="@TOOL_VERSION@+galaxy0">
    <description>Transposable Element Typer</description>
    <macros>
        <token name="@TOOL_VERSION@">1.1</token>
    </macros>
    <requirements>

            --flank_len '${flank_length}'
            --min_reads '${min_reads}'
            --min_each_strand '${min_each_strand}'
            --min_mapped_len '${min_mapped_len}'
            --min_qual '${min_qual}'
            #if $snp_profiles
              --snp_profiles '${snp_profiles}'
            #end if
            #if $struct_profiles
              --struct_profiles '${struct_profiles}'
            #end if
            --outprefix output
        ]]>
    </command>
    <inputs>

            <when value="paired">
                <param format="fastq,fastq.gz" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>
                <param format="fastq,fastq.gz" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>
            </when>
        </conditional>
        <param name="reference" type="data" format="fasta" label="Transposable Element Reference"/>
        <param name="flank_length" type="integer" min="4" value="5" max="16" label="Flank Length" help="Length of flanking region to extract."/>
        <param name="min_reads" type="integer" min="1" value="10" max="100" label="Minimum Reads" help="Minimum read number for including a specific flanking sequence."/>
        <param name="min_each_strand" type="integer" min="1" value="1" max="100" label="Minimum Reads (each strand)" help="Minimum read number for each strand for including a specific flanking sequence."/>
        <param name="min_mapped_len" type="integer" min="8" value="30" max="100" label="Minimum Mapped Length" help="Minimum length of mapping for a read to be used in determining flanking sequences. Higher values are more robust to spurious mapping. Lower values will recover more reads."/>
        <param name="min_qual" type="integer" min="0" value="10" max="100" label="Minimum quality" help="Minimum quality value across extracted flanking sequence." />
        <param name="snp_profiles" type="data" format="text" label="SNP Profiles" optional="true" />
        <param name="struct_profiles" type="data" format="text" label="Structural Variant Profiles" optional="true" />
        <param name="include_log" type="boolean" label="Include log in output"/>
    </inputs>
    <outputs>
        <data name="summary" format="tabular" from_work_dir="output_summary.txt" label="${tool.name} on ${on_string}: summary"/>
        <data name="snps" format="vcf" from_work_dir="output.vcf" label="${tool.name} on ${on_string}: SNPs"/>

            <conditional name="collection_paired">
                <param name="selector" value="paired" />
                <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
                <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
            </conditional>
            <param name="snp_profiles" value="Tn4401b_snp_profiles.txt" />
            <param name="struct_profiles" value="Tn4401b_struct_profiles.txt" />
            <output name="summary" file="output_summary_2.txt" />
        </test>
    </tests>
    <help>
      <![CDATA[

1:36093854bfc7

<tool id="tetyper" name="TETyper" version="@TOOL_VERSION@+galaxy1">
    <description>Transposable Element Typer</description>
    <macros>
        <token name="@TOOL_VERSION@">1.1</token>
    </macros>
    <requirements>

            --flank_len '${flank_length}'
            --min_reads '${min_reads}'
            --min_each_strand '${min_each_strand}'
            --min_mapped_len '${min_mapped_len}'
            --min_qual '${min_qual}'
            #if str( $snp_profiles_source.snp_profiles_source_selector ) == "tool_data_table":
                --snp_profiles '$snp_profiles_source.snp_profiles.fields.path'
            #elif str( $snp_profiles_source.snp_profiles_source_selector ) == 'history':
                --snp_profiles '$snp_profiles_source.snp_profiles'
            #end if
            #if str( $struct_profiles_source.struct_profiles_source_selector ) == "tool_data_table":
                --struct_profiles '$struct_profiles_source.struct_profiles.fields.path'
            #elif str( $struct_profiles_source.struct_profiles_source_selector ) == 'history':
                --struct_profiles '$struct_profiles_source.struct_profiles'
            #end if
            --outprefix output
        ]]>
    </command>
    <inputs>

            <when value="paired">
                <param format="fastq,fastq.gz" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>
                <param format="fastq,fastq.gz" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>
            </when>
        </conditional>
        <conditional name="snp_profiles_source">
            <param name="snp_profiles_source_selector" type="select"
                   label="Select a SNP profile from your history or use one from a tool data table?">
                <option value="No" selected="true">No SNP profile</option>
                <option value="tool_data_table">SNP profile from tool data table</option>
                <option value="history">SNP profile from history</option>
            </param>
            <when value="No"/>
            <when value="tool_data_table">
                <param name="snp_profiles" type="select" format="tabular" label="SNP Profile">
                    <options from_data_table="tetyper_snp_profiles">
                        <validator type="no_options" message="No TETyper SNP profiles are available" />
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="snp_profiles" type="data" format="tabular" label="SNP Profile"
                       help="A three-column tabular file with SNP profile definitions"/>
            </when>
        </conditional>
        <conditional name="struct_profiles_source">
            <param name="struct_profiles_source_selector" type="select"
                   label="Select a structural variant profile from your history or use one from a tool data table?">
                <option value="No" selected="true">No structural variant profile</option>
                <option value="tool_data_table">Structural variant profile from tool data table</option>
                <option value="history" selected="true">Structural variant profile from history</option>
            </param>
            <when value="No"/>
            <when value="tool_data_table">
                <param name="struct_profiles" type="select" format="tabular"
                       label="Structural Variant Profile">
                    <options from_data_table="tetyper_struct_profiles">
                        <validator type="no_options" message="No TETyper structural variant profiles are available" />
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="struct_profiles" type="data" format="tabular"
                       label="Structural Variant Profile"
                       help="A two-column tabular file with structural variant profile definitions"/>
            </when>
        </conditional>
        <param name="reference" type="data" format="fasta" label="Transposable Element Reference"/>
        <param name="flank_length" type="integer" min="4" value="5" max="16" label="Flank Length" help="Length of flanking region to extract."/>
        <param name="min_reads" type="integer" min="1" value="10" max="100" label="Minimum Reads" help="Minimum read number for including a specific flanking sequence."/>
        <param name="min_each_strand" type="integer" min="1" value="1" max="100" label="Minimum Reads (each strand)" help="Minimum read number for each strand for including a specific flanking sequence."/>
        <param name="min_mapped_len" type="integer" min="8" value="30" max="100" label="Minimum Mapped Length" help="Minimum length of mapping for a read to be used in determining flanking sequences. Higher values are more robust to spurious mapping. Lower values will recover more reads."/>
        <param name="min_qual" type="integer" min="0" value="10" max="100" label="Minimum quality" help="Minimum quality value across extracted flanking sequence." />
        <param name="include_log" type="boolean" label="Include log in output"/>
    </inputs>
    <outputs>
        <data name="summary" format="tabular" from_work_dir="output_summary.txt" label="${tool.name} on ${on_string}: summary"/>
        <data name="snps" format="vcf" from_work_dir="output.vcf" label="${tool.name} on ${on_string}: SNPs"/>

            <conditional name="collection_paired">
                <param name="selector" value="paired" />
                <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
                <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
            </conditional>
            <conditional name="snp_profiles_source">
                <param name="snp_profiles_source_selector" value="history" />
                <param name="snp_profiles" value="Tn4401b_snp_profiles.txt" />
            </conditional>
            <conditional name="struct_profiles_source">
                <param name="struct_profiles_source_selector" value="history" />
                <param name="struct_profiles" value="Tn4401b_struct_profiles.txt" />
            </conditional>
            <output name="summary" file="output_summary_2.txt" />
        </test>
        <test>
            <param name="reference" value="Tn4401b-1.fasta" />
            <conditional name="collection_paired">
                <param name="selector" value="paired" />
                <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
                <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
            </conditional>
            <conditional name="snp_profiles_source">
                <param name="snp_profiles_source_selector" value="tool_data_table" />
                <param name="snp_profiles" value="Tn4401b_snp_profiles" />
            </conditional>
            <conditional name="struct_profiles_source">
                <param name="struct_profiles_source_selector" value="tool_data_table" />
                <param name="struct_profiles" value="Tn4401b_struct_profiles" />
            </conditional>
            <output name="summary" file="output_summary_2.txt" />
        </test>
    </tests>
    <help>
      <![CDATA[