comparison collection_list_paired.xml @ 6:a0c8b2b25774 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 88ca36a41aa577ba888cee39cf81b176bf7e68db

5:66022ba24ac7

<tool id="rmarkdown_collection_list_paired" name="Collection type: list:paired" version="1.0.0">
    <requirements>
        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
        <requirement type="package" version="1.2">r-rmarkdown</requirement>
        <requirement type="package" version="0.3.5">r-htmltools</requirement>
        <requirement type="package" version="0.5.0">r-dplyr</requirement>
    </requirements>
    <description>
        Create a 'list:paired' dataset collection from a set of files in Galaxy history.
    </description>
    <stdio>
        <regex match="Execution halted"
               source="both"
               level="fatal"

        ]]>
    </command>
    <inputs>
        <param type="data" name="forward_file_list" multiple="true" label="forward inputs"/>
        <param type="data" name="reverse_file_list" multiple="true" label="reverse inputs"/>
        <param type="text" name="format" label="the format of input files (e.g., fastq, fastqsanger, fasta)"/>

        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
    </inputs>
    <outputs>
        <data format="html" name="report" label="Collection builder (list:paired collection)" />
        <collection type="list:paired" name="list_collection">
            <discover_datasets pattern="__name_and_ext__" directory="files_directory" visible="true"/>
        </collection>
    </outputs>
</tool>

6:a0c8b2b25774

<tool id="rmarkdown_collection_list_paired" name="Collection type (list:paired)" version="1.0.0">
    <requirements>
        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
        <requirement type="package" version="1.2">r-rmarkdown</requirement>
        <requirement type="package" version="0.3.5">r-htmltools</requirement>
        <requirement type="package" version="0.5.0">r-dplyr</requirement>
    </requirements>
    <description>
        Create a list of paired dataset collection from files in history.
    </description>
    <stdio>
        <regex match="Execution halted"
               source="both"
               level="fatal"

        ]]>
    </command>
    <inputs>
        <param type="data" name="forward_file_list" multiple="true" label="forward inputs"/>
        <param type="data" name="reverse_file_list" multiple="true" label="reverse inputs"/>
        <param type="text" name="format" label="the format (extension) of input files (e.g., fastq, fastqsanger, fasta)"/>

        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
    </inputs>
    <outputs>
        <data format="html" name="report" label="Collection builder (list:paired collection)" />
        <collection type="list:paired" name="list_collection">
            <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.(?P&lt;ext&gt;[^\._]+)?" directory="files_directory"/>
        </collection>
    </outputs>
</tool>