view biaftplink.xml @ 0:3085096f2b99 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 04eb6bf2ffe44b87f8c12134ac3bee33656f0673

<tool id="bia_download" name="FTP Link for Bioimage Archive" version="@VERSION@+galaxy0" profile="22.05">
    <description>Download images from Bioimage Archive</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive">
<![CDATA[
        wget -r 'ftp://ftp.ebi.ac.uk/biostudies/$mode/$path'/Files; 
        #if '$ftp_output'
            #set study = $path.split('/')[-1].rstrip('/')
            curl https://www.ebi.ac.uk/biostudies/api/v1/studies/$study/info -s |jq -r .ftpLink >>ftpLink.txt
        #end if
]]>
    </command>
    <inputs>
    <param name="mode" type="text" label="Storage mode" help="The storage mode, can be either nfs or fire."/>
    <param name="path" type="text" label="The path of accession. e.g. S-BIAD/570/S-BIAD570 "/>
        <param name="ftplink_output" type="boolean" label="Generate FTP links?" help="If set, a file containing FTP links associated with the accession will be generated." />
    </inputs>
    <outputs>
        <data name="images" format="tiff">
            <discover_datasets pattern="__name_and_ext__" format="tif,tiff" directory="ftp.ebi.ac.uk" visible="true" recurse="true" />
        </data>
        <data format="txt" name="ftplinks" from_work_dir="ftpLink.txt" label="FTP Links">
            <filter>ftplink_output</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs='1'>
            <param name="mode" value="fire" />
            <param name="path" value="S-BIAD/961/S-BIAD961" />
            <param name="ftplink_output" value="False" />
            <output name="images">
                <discovered_dataset designation="Study_Component-4_mznanog_mCherry-AAT" ftype="tif">
                    <assert_contents><has_size value="14092624" /></assert_contents>
                </discovered_dataset>
            </output>
        </test>
        <test expect_num_outputs='2'>
            <param name="mode" value="fire" />
            <param name="path" value="S-BIAD/961/S-BIAD961" />
            <param name="ftplink_output" value="True" />
            <output name="images">
                 <discovered_dataset designation="Study_Component-4_mznanog_mCherry-AAT" ftype="tif">
                     <assert_contents><has_size value="14092624" /></assert_contents>
                </discovered_dataset>
            </output>
               <output name="ftplinks" ftype="txt" file="ftpLink.txt" lines_diff="0" />
            </test>
    </tests>
    <help>
<![CDATA[
        **What it does**
        This tool downloads images from the Bioimage Archive and optionally outputs FTP links associated with the input accession.
]]>
    </help>
    <expand macro="citations" />
</tool>