|
4
|
1 <tool id="ts_import_1" name="Import Data from TrustStore" vertion="0.1"> <!-- tool_type="data_source"> -->
|
|
|
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>
|
|
|
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 $output</command>
|
|
|
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" />
|
|
|
70 <param name="filename" type="text" label="Filename" help="e.g.: export1.bam. Leave empty if 'just list files' is chosen above." value="" size="20" />
|
|
4
|
71 </inputs>
|
|
|
72 <outputs>
|
|
5
|
73 <data name="output" 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>
|
|
|
116 <requirement type="python-module">py_ts</requirement>
|
|
|
117 <requirement type="binary" version="1.0.0">openssl</requirement>
|
|
|
118 </requirements>
|
|
|
119
|
|
|
120 <help>
|
|
|
121 This tool lets users import data they have uploaded to the TrustStore system.
|
|
|
122
|
|
|
123 Upload files to TrustStore using the desktop client.
|
|
|
124 </help>
|
|
|
125 </tool> |
