Mercurial > repos > matt-shirley > ncbi_sra_toolkit
annotate sra_pileup.xml @ 26:7d80b2b24270
Set config values for caching.
| author | Matt Shirley <mdshw5@gmail.com> |
|---|---|
| date | Mon, 30 Mar 2015 22:11:38 -0400 |
| parents | 393a04ec0fa9 |
| children | fdc981664a43 |
| rev | line source |
|---|---|
| 2 | 1 <tool id="sra_pileup" name="Generate pileup format" version="1.1.1"> |
| 2 <description> from NCBI sra.</description> | |
|
25
393a04ec0fa9
Update tool requirement versions.
Matt Shirley <mdshw5@gmail.com>
parents:
2
diff
changeset
|
3 <command>sra-pileup --log-level fatal |
| 2 | 4 #if str( $region ) != "": |
| 5 --aligned-region $region | |
| 6 #end if | |
| 7 #if str( $minMapq ) != "": | |
| 8 --minmapq $minMapq | |
| 9 #end if | |
| 10 #if $input.input_select == "file": | |
| 11 $input.file | |
| 12 #elif $input.input_select == "accession_number": | |
|
25
393a04ec0fa9
Update tool requirement versions.
Matt Shirley <mdshw5@gmail.com>
parents:
2
diff
changeset
|
13 $input.accession |
| 2 | 14 #elif $input.input_select == "text": |
| 15 `cat $input.text` | |
| 16 #end if | |
| 17 > $output</command> | |
| 18 <version_string>sra-pileup --version</version_string> | |
| 19 <inputs> | |
| 20 <conditional name="input"> | |
| 21 <param name="input_select" type="select" label="select input type"> | |
| 22 <option value="accession_number">SRR accession</option> | |
| 23 <option value="file">SRA archive in current history</option> | |
| 24 <option value="text">text file containing SRR accession</option> | |
| 25 </param> | |
| 26 <when value="file"> | |
| 27 <param format="sra" name="file" type="data" label="sra archive"/> | |
| 28 </when> | |
| 29 <when value="accession_number"> | |
| 30 <param format="text" name="accession" type="text" label="accession"/> | |
| 31 </when> | |
| 32 <when value="text"> | |
| 33 <param format="txt" name="text" type="data" label="text file"/> | |
| 34 </when> | |
| 35 </conditional> | |
| 36 <param format="text" name="region" type="text" label="aligned region"/> | |
| 37 <param format="text" name="minMapq" type="text" label="minimum mapping quality"/> | |
| 38 </inputs> | |
| 39 <outputs> | |
| 40 <data format="pileup" name="output"/> | |
| 41 </outputs> | |
| 42 <requirements> | |
|
25
393a04ec0fa9
Update tool requirement versions.
Matt Shirley <mdshw5@gmail.com>
parents:
2
diff
changeset
|
43 <requirement type="package" version="2.4.5">sra_toolkit</requirement> |
| 2 | 44 </requirements> |
| 45 <help> | |
|
25
393a04ec0fa9
Update tool requirement versions.
Matt Shirley <mdshw5@gmail.com>
parents:
2
diff
changeset
|
46 This tool produces pileup format from sra archives using sra-pileup. |
|
393a04ec0fa9
Update tool requirement versions.
Matt Shirley <mdshw5@gmail.com>
parents:
2
diff
changeset
|
47 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. |
| 2 | 48 The sra-pileup program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. |
| 49 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. | |
| 50 </help> | |
| 51 </tool> |