Mercurial > repos > cathywise > truststore_import
diff TrustStoreGalaxyImport.xml @ 4:32d9b3343955
Toooool upload.
| author | Catherine Wise <catherine.wise@csiro.au> |
|---|---|
| date | Thu, 12 Dec 2013 13:07:45 +1100 |
| parents | |
| children | 159d2159e745 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/TrustStoreGalaxyImport.xml Thu Dec 12 13:07:45 2013 +1100 @@ -0,0 +1,123 @@ +<tool id="ts_import_1" name="Import Data from TrustStore" vertion="0.1"> <!-- 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 https://tstest-kms.it.csiro.au/kmscolab_3_0 https://tstest-ims.it.csiro.au/ims_3_0/services/IMS $username $password desktop cpU92F1PT7VOCANjSknuCDp4DrubmujoBaF6b0miz8OpKNokEbGMHCaSFK5/lISbBmaaGVCgeADI2A39F3Hkeg== $storename $path $filename $output</command> + <inputs> + <param name="file_type" type="select" label="File Format" help="Which format is the data you're downloading?"> + <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="kms username" value="user" size="20" > + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + <param name="password" type="text" label="password" help="kms password" value="password" size="1"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" 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="File name" help="e.g.: export1.bam" value="1.png" size="20" /> + </inputs> + <outputs> + <data name="output" format="ab1"> + <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" /> + </change_format> + </data> + </outputs> + + <tests> + <test> + </test> + </tests> + + <requirements> + <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> \ No newline at end of file