Mercurial > repos > yating-l > ucsc_trix_index_generator
annotate trixIndex.xml @ 1:c1ebe32249b0 draft default tip
planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
| author | yating-l |
|---|---|
| date | Mon, 06 Nov 2017 15:38:14 -0500 |
| parents | 45cb248771d2 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool id="ucsc_trix_index_generator" name="UCSC Trix Index Generator" version="1.0"> | |
| 3 <description>Create UCSC Trix index from a tab-delimited text file or a Fasta file</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement> | |
| 6 </requirements> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 #if $input_type.input_type_selector == "fasta": | |
| 9 python $__tool_directory__/extractHeaders.py $input_type.input_file tab_file | |
| 10 && | |
| 11 ixIxx tab_file ${index_ix} ${index_ixx} | |
| 12 #else: | |
| 13 ixIxx $input_type.input_file ${index_ix} ${index_ixx} | |
| 14 #end if | |
| 15 ]]></command> | |
| 16 <inputs> | |
| 17 <conditional name="input_type"> | |
| 18 <param name="input_type_selector" type="select" label="Choose the format" argument="--file_type"> | |
| 19 <option value="tab">Tabular</option> | |
| 20 <option value="fasta" selected="True">Fasta</option> | |
| 21 </param> | |
| 22 <when value="tab"> | |
| 23 <param name="input_file" type="data" format="tabular" label="Tabular File" argument="-f"/> | |
| 24 </when> | |
| 25 <when value="fasta"> | |
| 26 <param name="input_file" type="data" format="fasta" label="Fasta File" argument="-f"/> | |
| 27 </when> | |
| 28 </conditional> | |
| 29 </inputs> | |
| 30 <outputs> | |
|
1
c1ebe32249b0
planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
0
diff
changeset
|
31 <collection name="trix_index" type="list" label="${tool.name} on ${on_string}:Trix index"> |
|
c1ebe32249b0
planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
0
diff
changeset
|
32 <data name="index_ix" format="txt" /> |
|
c1ebe32249b0
planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
0
diff
changeset
|
33 <data name="index_ixx" format="txt" /> |
| 0 | 34 </collection> |
| 35 </outputs> | |
| 36 <tests> | |
| 37 <test> | |
| 38 <param name="input_type_selector" value="fasta" /> | |
| 39 <param name="input_file" value="dmel-hits-translation-r6.11.fasta" /> | |
| 40 <output_collection name="trix_index" type="list"> | |
|
1
c1ebe32249b0
planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
0
diff
changeset
|
41 <element name="index_ix" value="out.ix" /> |
|
c1ebe32249b0
planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
0
diff
changeset
|
42 <element name="index_ixx" value="out.ixx" /> |
| 0 | 43 </output_collection> |
| 44 </test> | |
| 45 <test> | |
| 46 <param name="input_type_selector" value="tab" /> | |
| 47 <param name="input_file" value="dmel-hits-tab" /> | |
| 48 <output_collection name="trix_index" type="list"> | |
|
1
c1ebe32249b0
planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
0
diff
changeset
|
49 <element name="index_ix" value="out.ix" /> |
|
c1ebe32249b0
planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
yating-l
parents:
0
diff
changeset
|
50 <element name="index_ixx" value="out.ixx" /> |
| 0 | 51 </output_collection> |
| 52 </test> | |
| 53 </tests> | |
| 54 <help> | |
| 55 <![CDATA[ | |
| 56 UCSC Trix Index Generator | |
| 57 ========================== | |
| 58 | |
| 59 Generate UCSC Trix index from a Fasta file or a Tabular file | |
| 60 ------------------------------------------------------------- | |
| 61 | |
| 62 ixIxx - Create indices for simple line-oriented file of format | |
| 63 | |
| 64 Reference: https://genome.ucsc.edu/goldenpath/help/trix.html | |
| 65 | |
| 66 Source code: | |
| 67 ============ | |
| 68 | |
| 69 http://hgdownload.cse.ucsc.edu/admin/exe/ | |
| 70 | |
| 71 ]]></help> | |
| 72 <citations> | |
| 73 <citation type="bibtex"> | |
| 74 @article{Kent01062002, | |
| 75 author = {Kent, W. James and Sugnet, Charles W. and Furey, Terrence S. and Roskin, Krishna M. and Pringle, Tom H. and Zahler, Alan M. and Haussler, and David}, | |
| 76 title = {The Human Genome Browser at UCSC}, | |
| 77 volume = {12}, | |
| 78 number = {6}, | |
| 79 pages = {996-1006}, | |
| 80 year = {2002}, | |
| 81 doi = {10.1101/gr.229102}, | |
| 82 URL = {http://genome.cshlp.org/content/12/6/996.abstract}, | |
| 83 eprint = {http://genome.cshlp.org/content/12/6/996.full.pdf+html}, | |
| 84 journal = {Genome Research} | |
| 85 } | |
| 86 </citation> | |
| 87 </citations> | |
| 88 </tool> | |
| 89 | |
| 90 | |
| 91 | |
| 92 | |
| 93 |