Mercurial > repos > cathywise > truststore_import
annotate TrustStoreGalaxyImport.xml @ 36:8e8a88fe0f4f
GRRR.
| author | Catherine Wise <catherine.wise@csiro.au> |
|---|---|
| date | Thu, 23 Jan 2014 15:05:41 +1100 |
| parents | 3bed3ea2c474 |
| children | 2ced2ca1c758 |
| rev | line source |
|---|---|
| 30 | 1 <tool id="ts_import_1" name="Import Data from TrustStore" vertion="0.1" force_history_refresh="True"> <!-- tool_type="data_source"> --> |
| 4 | 2 <description> secure cloud storage.</description> |
| 3 <stdio> | |
| 4 <exit_code range="2" err_level="fatal" description="Could not find store with supplied name." /> | |
| 5 <exit_code range="3" err_level="fatal" description="Could not find supplied path in store." /> | |
| 6 <exit_code range="4" err_level="fatal" description="Could not find supplied filename in store at path." /> | |
| 7 <exit_code range="5" err_level="fatal" description="Bad credentials supplied. See stdout for more information." /> | |
| 8 </stdio> | |
|
31
6e2dba73eebd
Undo multi file ugh.
Catherine Wise <catherine.wise@csiro.au>
parents:
30
diff
changeset
|
9 <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 $output1 </command> <!-- $output1.id $file_type </command> $__new_file_path__</command> --> |
| 4 | 10 <inputs> |
| 11 <param name="file_type" type="select" label="File Format" help="Which format is the data you're downloading?"> | |
| 5 | 12 <option value="just list files"/> |
| 4 | 13 <option value="ab1"/> |
| 14 <option value="axt"/> | |
| 15 <option value="bam"/> | |
| 16 <option value="bed"/> | |
| 17 <option value="coverage" /> | |
| 18 <option value="customtrack" /> | |
| 19 <option value="csfasta" /> | |
| 20 <option value="fasta" /> | |
| 21 <option value="eland" /> | |
| 22 <option value="fastq" /> | |
| 23 <option value="fasqsanger" /> | |
| 24 <option value="gtf" /> | |
| 25 <option value="gff" /> | |
| 26 <option value="gff3" /> | |
| 27 <option value="genetrack" /> | |
| 28 <option value="interval" /> | |
| 29 <option value="laj" /> | |
| 30 <option value="lav" /> | |
| 31 <option value="maf" /> | |
| 32 <option value="pileup" /> | |
| 33 <option value="qualsolid" /> | |
| 34 <option value="qualsolexa" /> | |
| 35 <option value="sam"/> | |
| 36 <option value="scf"/> | |
| 37 <option value="sff"/> | |
| 38 <option value="tabular" /> | |
| 39 <option value="taxonomy" /> | |
| 40 <option value="txt"/> | |
| 41 <option value="wig"/> | |
| 42 <option value="xml"/> | |
| 43 </param> | |
| 44 <!-- <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" /> | |
| 45 <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" /> --> | |
| 5 | 46 <param name="username" type="text" label="Username" help="Your KMS username, e.g. jo.blogs@workplace.com" value="user" size="20" > |
| 4 | 47 <sanitizer> |
| 48 <valid initial="string.printable"> | |
| 49 <remove value="'"/> | |
| 50 </valid> | |
| 51 <mapping initial="none"> | |
| 52 <add source="'" target="__sq__"/> | |
| 53 </mapping> | |
| 54 </sanitizer> | |
| 55 </param> | |
| 5 | 56 <param name="password" type="text" label="Password" help="Your KMS password" value="password" size="1"> |
| 4 | 57 <sanitizer> |
| 58 <valid initial="string.printable"> | |
| 59 <remove value="'"/> | |
| 60 </valid> | |
| 61 <mapping initial="none"> | |
| 62 <add source="'" target="__sq__"/> | |
| 63 </mapping> | |
| 64 </sanitizer> | |
| 65 </param> | |
| 66 <!-- <param name="client_key" type="text" label="client key" help="kms client name" value="my-trusted-client-with-secret" size="20" /> --> | |
| 67 <!-- <param name="client_secret" type="text" label="client secret" help="kms client secret" value="somesecret" size="20" /> --> | |
| 68 <param name="storename" type="text" label="Store Name" help="e.g.: My Galaxy Store" value="galaxy" size="20" /> | |
| 5 | 69 <param name="path" type="text" label="Path in Store" help="e.g.: /rawdata/feb2014/, leave as / for top level files" value="/" size="20" /> |
| 32 | 70 <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" /> |
| 4 | 71 </inputs> |
| 72 <outputs> | |
| 30 | 73 <data name="output1" format="txt"> |
| 4 | 74 <change_format> |
| 75 <when input="file_type" value="ab1" format="ab1" /> | |
| 76 <when input="file_type" value="axt" format="axt" /> | |
| 77 <when input="file_type" value="bam" format="bam" /> | |
| 78 <when input="file_type" value="bed" format="bed" /> | |
| 79 <when input="file_type" value="coverage" format="coverage" /> | |
| 80 <when input="file_type" value="customtrack" format="customtrack" /> | |
| 81 <when input="file_type" value="csfasta" format="csfasta" /> | |
| 82 <when input="file_type" value="fasta" format="fasta" /> | |
| 83 <when input="file_type" value="eland" format="eland" /> | |
| 84 <when input="file_type" value="fastq" format="fastq" /> | |
| 85 <when input="file_type" value="fasqsanger" format="fastqsanger" /> | |
| 86 <when input="file_type" value="gtf" format="gtf" /> | |
| 87 <when input="file_type" value="gff" format="gff" /> | |
| 88 <when input="file_type" value="gff3" format="gff3" /> | |
| 89 <when input="file_type" value="genetrack" format="genetrack" /> | |
| 90 <when input="file_type" value="interval" format="interval" /> | |
| 91 <when input="file_type" value="laj" format="laj" /> | |
| 92 <when input="file_type" value="lav" format="lav" /> | |
| 93 <when input="file_type" value="maf" format="maf" /> | |
| 94 <when input="file_type" value="pileup" format="pileup" /> | |
| 95 <when input="file_type" value="qualsolid" format="qualsolid" /> | |
| 96 <when input="file_type" value="qualsolexa" format="qualsolexa" /> | |
| 97 <when input="file_type" value="sam" format="sam" /> | |
| 98 <when input="file_type" value="scf" format="scf" /> | |
| 99 <when input="file_type" value="sff" format="sff" /> | |
| 100 <when input="file_type" value="tabular" format="tabular" /> | |
| 101 <when input="file_type" value="taxonomy" format="taxonomy" /> | |
| 102 <when input="file_type" value="txt" format="txt" /> | |
| 103 <when input="file_type" value="wig" format="wig" /> | |
| 104 <when input="file_type" value="xml" format="xml" /> | |
| 5 | 105 <when input="file_type" value="just list files" format="txt"/> |
| 4 | 106 </change_format> |
| 107 </data> | |
| 108 </outputs> | |
| 109 | |
| 110 <tests> | |
| 111 <test> | |
| 112 </test> | |
| 113 </tests> | |
| 114 | |
| 115 <requirements> | |
| 36 | 116 <requirement type="package" version="0.2.6">py_ts</requirement> |
|
7
22b0e927b7fe
Fiddle with dependencies.
Catherine Wise <catherine.wise@csiro.au>
parents:
5
diff
changeset
|
117 <requirement type="python_module">py_ts</requirement> |
| 4 | 118 <requirement type="binary" version="1.0.0">openssl</requirement> |
| 119 </requirements> | |
| 120 | |
| 121 <help> | |
| 122 This tool lets users import data they have uploaded to the TrustStore system. | |
| 123 | |
| 124 Upload files to TrustStore using the desktop client. | |
| 125 </help> | |
| 126 </tool> |