comparison abundance_estimates_to_matrix.xml @ 5:8b5039bdf1f6 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933

4:1fc32fd3fb3f

<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.1">
    <description>for a de novo assembly of RNA-Seq data by Trinity</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="3.14.0">bioconductor-edger</requirement>
        <requirement type="package" version="0.7.2">salmon</requirement>
    </expand>
    <expand macro="stdio"/>
    <command><![CDATA[
        #import re
        #for $entry in $samples:
            ln -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' &&
        #end for

        abundance_estimates_to_matrix.pl

        --est_method ${est_method}

5:8b5039bdf1f6

<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.0">
    <description>for a de novo assembly of RNA-Seq data by Trinity</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="3.16.5">bioconductor-edger</requirement>
        <!-- Cannot update to salmon 0.8.2 because in Bioconda it requires icu 58, while r-base 3.3.1 requires icu 54 -->
        <requirement type="package" version="0.8.1">salmon</requirement>
    </expand>
    <command detect_errors="aggressive"><![CDATA[
        #import re
        #for $entry in $samples:
            ln -f -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' &&
        #end for

        abundance_estimates_to_matrix.pl

        --est_method ${est_method}