Mercurial > repos > jackcurragh > trips_viz_bam_to_sqlite

comparison trips_bam_to_sqlite/trips_bam_to_sqlite.xml @ 20:5948fc162f8c draft default tip

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author jackcurragh
date Tue, 08 Aug 2023 11:00:26 +0000
parents d8cc5dbc9fa8
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19:d8cc5dbc9fa8 20:5948fc162f8c
1 <tool id="bam_to_sqlite" name="BAM to Sqlite" version="1.8a"> 1 <tool id="bam_to_sqlite" name="BAM to Sqlite" version="1.7">
2 <description>Convert BAM file to SQLITE for Trips-Viz</description> 2 <description>Convert BAM file to SQLITE for Trips-Viz</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.19.0">pysam</requirement> 4 <requirement type="package" version="0.19.0">pysam</requirement>
5 <requirement type="package" version="1.7.0">sqlitedict</requirement> 5 <requirement type="package" version="1.7.0">sqlitedict</requirement>
6 <requirement type="package" version="3.37.1">sqlite</requirement> 6 <requirement type="package" version="3.37.1">sqlite</requirement>
22 <option value="builtin">Use a built-in SQLITE</option> 22 <option value="builtin">Use a built-in SQLITE</option>
23 <option value="history">Use one from the history</option> 23 <option value="history">Use one from the history</option>
24 </param> 24 </param>
25 <when value="builtin"> 25 <when value="builtin">
26 <param name="input2_builtin" type="select" format="sqlite" label="Select a SQLITE" help="if your organism of interest is not listed - contact RiboGalaxy team"> 26 <param name="input2_builtin" type="select" format="sqlite" label="Select a SQLITE" help="if your organism of interest is not listed - contact RiboGalaxy team">
27 <options from_data_table="sqlites_upd1"> 27 <options from_data_table="sqlites">
28 <filter type="sort_by" column="2" /> 28 <filter type="sort_by" column="2" />
29 <validator type="no_options" message="No built-ins are available" /> 29 <validator type="no_options" message="No built-ins are available" />
30 </options> 30 </options>
31 </param> 31 </param>
32 </when> 32 </when>
33 <when value="history"> 33 <when value="history">
34 <param name="input2_file" type="data" format="sqlite" label="SQLITE File" /> 34 <param name="input2_file" type="data" format="sqlite" label="SQLITE File" />
35 </when> 35 </when>
36 </conditional> 36 </conditional>
37 37
38 <param name="input3" type="text" label="Description of this sample" /> 38 <param name="input3" type="text" label="Description of this sample (Required)"/>
39 </inputs> 39 </inputs>
40 <outputs> 40 <outputs>
41 <data name="output1" format="sqlite"/> 41 <data name="output1" format="sqlite"/>
42 </outputs> 42 </outputs>
43 <tests> 43 <tests>