view TrustStoreGalaxyImport.xml @ 39:64e06297da39 default tip

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<tool id="ts_import_1" name="Import Data from TrustStore" vertion="0.1" force_history_refresh="True"> <!-- tool_type="data_source"> -->
    <description> secure cloud storage.</description>
    <stdio>
        <exit_code range="2" err_level="fatal" description="Could not find store with supplied name." />
        <exit_code range="3" err_level="fatal" description="Could not find supplied path in store." />
        <exit_code range="4" err_level="fatal" description="Could not find supplied filename in store at path." />
        <exit_code range="5" err_level="fatal" description="Bad credentials supplied. See stdout for more information." />
    </stdio>
    <command interpreter="python">TrustStoreGalaxyImport.py $username $password $storename $path $file_type $filename $output1 $output1.id $__new_file_path__</command>
    <inputs>
        <param name="file_type" type="select" label="File Format" help="Which format is the data you're downloading?">
            <option value="just_list_files"/>
            <option value="ab1"/>
            <option value="axt"/>
            <option value="bam"/>
            <option value="bed"/>
            <option value="coverage" />
            <option value="customtrack" />
            <option value="csfasta" />
            <option value="fasta" />
            <option value="eland" />
            <option value="fastq" />
            <option value="fasqsanger" />
            <option value="gtf" />
            <option value="gff" />
            <option value="gff3" />
            <option value="genetrack" />
            <option value="interval" />
            <option value="laj" />
            <option value="lav" />
            <option value="maf" />
            <option value="pileup" />
            <option value="qualsolid" />
            <option value="qualsolexa" />
            <option value="sam"/>
            <option value="scf"/>
            <option value="sff"/>
            <option value="tabular" />
            <option value="taxonomy" />
            <option value="txt"/>
            <option value="wig"/>
            <option value="xml"/>
        </param>
        <!-- <param name="kms_url" type="text" label="kms url" help="the remote url for your key management service" value="http://localhost:8080/TSSKeyManagementService-Collaboration" size="200" />
        <param name="ims_url" type="text" label="ims url" help="the remote url for your integrity management service" value="http://localhost:8080/TSSIntegrityManagementService/services/IMS" size="200" /> -->
        <param name="username" type="text" label="Username" help="Your KMS username, e.g. [e-mail]" value="user" size="20" >
            <sanitizer>
                <valid initial="string.printable">
                    <remove value="&apos;"/>
                </valid>
                <mapping initial="none">
                    <add source="&apos;" target="__sq__"/>
                </mapping>
            </sanitizer>
        </param>
        <param name="password" type="text" label="Password" help="Your KMS password" value="password" size="1">
            <sanitizer>
                <valid initial="string.printable">
                    <remove value="&apos;"/>
                </valid>
                <mapping initial="none">
                    <add source="&apos;" target="__sq__"/>
                </mapping>
            </sanitizer>
        </param>
        <!-- <param name="client_key" type="text" label="client key" help="kms client name" value="my-trusted-client-with-secret" size="20" /> -->
        <!-- <param name="client_secret" type="text" label="client secret" help="kms client secret" value="somesecret" size="20" /> -->
        <param name="storename" type="text" label="Store Name" help="e.g.: My Galaxy Store" value="galaxy" size="20" />
        <param name="path" type="text" label="Path in Store" help="e.g.: /rawdata/feb2014/, leave as / for top level files" value="/" size="20" />
        <param name="filename" type="text" label="Filename(s)" help="e.g.: export1.bam,export2.bam Comma seperated. Leave empty if 'just list files' is chosen above." value="" size="40" />
    </inputs>
    <outputs>
        <data name="output1" format="txt">
            <change_format>
                <when input="file_type" value="ab1" format="ab1" />
                <when input="file_type" value="axt" format="axt" />
                <when input="file_type" value="bam" format="bam" />
                <when input="file_type" value="bed" format="bed" />
                <when input="file_type" value="coverage" format="coverage" />
                <when input="file_type" value="customtrack" format="customtrack" />
                <when input="file_type" value="csfasta" format="csfasta" />
                <when input="file_type" value="fasta" format="fasta" />
                <when input="file_type" value="eland" format="eland" />
                <when input="file_type" value="fastq" format="fastq" />
                <when input="file_type" value="fasqsanger" format="fastqsanger" />
                <when input="file_type" value="gtf" format="gtf" />
                <when input="file_type" value="gff" format="gff" />
                <when input="file_type" value="gff3" format="gff3" />
                <when input="file_type" value="genetrack" format="genetrack" />
                <when input="file_type" value="interval" format="interval" />
                <when input="file_type" value="laj" format="laj" />
                <when input="file_type" value="lav" format="lav" />
                <when input="file_type" value="maf" format="maf" />
                <when input="file_type" value="pileup" format="pileup" />
                <when input="file_type" value="qualsolid" format="qualsolid" />
                <when input="file_type" value="qualsolexa" format="qualsolexa" />
                <when input="file_type" value="sam" format="sam" />
                <when input="file_type" value="scf" format="scf" />
                <when input="file_type" value="sff" format="sff" />
                <when input="file_type" value="tabular" format="tabular" />
                <when input="file_type" value="taxonomy" format="taxonomy" />
                <when input="file_type" value="txt" format="txt" />
                <when input="file_type" value="wig" format="wig" />
                <when input="file_type" value="xml" format="xml" />
                <when input="file_type" value="just_list_files" format="txt"/>
            </change_format>
        </data>
    </outputs>

    <tests>
        <test>
        </test>
    </tests>

    <requirements>
        <requirement type="package" version="0.3">py_ts</requirement>
        <requirement type="python_module">py_ts</requirement>
        <requirement type="binary" version="1.0.0">openssl</requirement>
    </requirements>

    <help>
This tool lets users import data they have uploaded to the TrustStore system.

Upload files to TrustStore using the desktop client.
    </help>
</tool>