root/galaxy-central/tools/data_source/microbial_import.xml

リビジョン 2, 5.3 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="microbial_import1" name="Get Microbial Data">
2  <command interpreter="python">microbial_import.py $CDS,$tRNA,$rRNA,$sequence,$GeneMark,$GeneMarkHMM,$Glimmer3 $output ${GALAXY_DATA_INDEX_DIR}/microbial_data.loc</command>
3  <inputs>
4      <param name="kingdom" type="select" label="Select the Desired Kingdom">
5        <options from_file="microbial_data.loc" startswith="ORG">
6          <column name="name" index="3"/>
7          <column name="value" index="3"/>
8          <filter type="unique_value" name="unique" column="3"/>
9        </options>
10      </param>
11      <param name="org" type="select" label="Select the Desired Organism">
12        <options from_file="microbial_data.loc" startswith="ORG">
13          <column name="name" index="2"/>
14          <column name="value" index="1"/>
15          <filter type="param_value" ref="kingdom" name="kingdom" column="3"/>
16          <filter type="sort_by" column="2"/>
17        </options>
18      </param>
19      <param name="CDS" type="select" label="Select Desired Coding Sequences" display="checkboxes" multiple="True">
20        <options from_file="microbial_data.loc" startswith="DATA">
21          <column name="name" index="3"/>
22          <column name="value" index="1"/>
23          <column name="feature" index="4"/>
24          <filter type="param_value" ref="org" name="kingdom" column="2"/>
25          <filter type="static_value" name="feature" value="CDS" column="4"/>
26        </options>
27      </param>
28      <param name="tRNA" type="select" label="Select Desired tRNA" display="checkboxes" multiple="True">
29        <options from_file="microbial_data.loc" startswith="DATA">
30          <column name="name" index="3"/>
31          <column name="value" index="1"/>
32          <column name="feature" index="4"/>
33          <filter type="param_value" ref="org" name="kingdom" column="2"/>
34          <filter type="static_value" name="feature" value="tRNA" column="4"/>
35        </options>
36      </param>
37      <param name="rRNA" type="select" label="Select Desired rRNA" display="checkboxes" multiple="True">
38        <options from_file="microbial_data.loc" startswith="DATA">
39          <column name="name" index="3"/>
40          <column name="value" index="1"/>
41          <column name="feature" index="4"/>
42          <filter type="param_value" ref="org" name="kingdom" column="2"/>
43          <filter type="static_value" name="feature" value="rRNA" column="4"/>
44        </options>
45      </param>
46      <param name="sequence" type="select" label="Select Desired DNA Sequences" display="checkboxes" multiple="True">
47        <options from_file="microbial_data.loc" startswith="DATA">
48          <column name="name" index="3"/>
49          <column name="value" index="1"/>
50          <column name="feature" index="4"/>
51          <filter type="param_value" ref="org" name="kingdom" column="2"/>
52          <filter type="static_value" name="feature" value="sequence" column="4"/>
53        </options>
54      </param>
55      <param name="GeneMark" type="select" label="Select Desired GeneMark Annotations" display="checkboxes" multiple="True">
56        <options from_file="microbial_data.loc" startswith="DATA">
57          <column name="name" index="3"/>
58          <column name="value" index="1"/>
59          <column name="feature" index="4"/>
60          <filter type="param_value" ref="org" name="kingdom" column="2"/>
61          <filter type="static_value" name="feature" value="GeneMark" column="4"/>
62        </options>
63      </param>
64      <param name="GeneMarkHMM" type="select" label="Select Desired GeneMarkHMM Annotations" display="checkboxes" multiple="True">
65        <options from_file="microbial_data.loc" startswith="DATA">
66          <column name="name" index="3"/>
67          <column name="value" index="1"/>
68          <column name="feature" index="4"/>
69          <filter type="param_value" ref="org" name="kingdom" column="2"/>
70          <filter type="static_value" name="feature" value="GeneMarkHMM" column="4"/>
71        </options>
72      </param>
73      <param name="Glimmer3" type="select" label="Select Desired Glimmer3 Annotations" display="checkboxes" multiple="True">
74        <options from_file="microbial_data.loc" startswith="DATA">
75          <column name="name" index="3"/>
76          <column name="value" index="1"/>
77          <column name="feature" index="4"/>
78          <filter type="param_value" ref="org" name="kingdom" column="2"/>
79          <filter type="static_value" name="feature" value="Glimmer3" column="4"/>
80        </options>
81      </param>
82  </inputs>
83  <outputs>
84    <data format="bed" name="output"/>
85  </outputs>
86  <code file="microbial_import_code.py"/>
87  <help>
88
89This tool will allow you to obtain various genomic datasets for any completed Microbial Genome Project as listed at NCBI_.
90
91.. _NCBI: http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?view=1
92
93Current datasets available include
94  1. CDS
95  2. tRNA
96  3. rRNA
97  4. FASTA Sequences
98  5. GeneMark Annotations
99  6. GeneMarkHMM Annotations
100  7. Glimmer3 Annotations
101
102-----
103
104Organisms in **bold** are available at the UCSC Browser.
105
106-----
107
108.. class:: infomark
109
110**Note:** Having trouble locating your organism?  Click here_ for a list of available species and their location.
111
112.. _here: http://bitbucket.org/galaxy/galaxy-central/wiki/Microbes
113
114  </help>
115</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。