Mercurial > repos > cpt > cpt_intron_detection
comparison cpt_intron_detect/intron_detection.xml @ 0:1a19092729be draft
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| author | cpt |
|---|---|
| date | Fri, 13 May 2022 05:08:54 +0000 |
| parents | |
| children | e0e294a1ccdd |
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| -1:000000000000 | 0:1a19092729be |
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| 1 <?xml version="1.1"?> | |
| 2 <tool id="edu.tamu.cpt2.phage.intron_detection" name="Interrupted gene detection tool" version="19.1.0.0"> | |
| 3 <description>based on nearby protein blast results</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 <import>cpt-macros.xml</import> | |
| 7 </macros> | |
| 8 <requirements> | |
| 9 <requirement type="package" version="3.6">python</requirement> | |
| 10 <requirement type="package" version="1.77">biopython</requirement> | |
| 11 <requirement type="package" version="1.1.3">cpt_gffparser</requirement> | |
| 12 </requirements> | |
| 13 <command detect_errors="aggressive"><![CDATA[ | |
| 14 python $__tool_directory__/intron_detection.py | |
| 15 | |
| 16 "$gff3_data" | |
| 17 "$blast" | |
| 18 --minimum $minimum | |
| 19 --maximum $maximum | |
| 20 --idThresh $idThresh | |
| 21 > $output]]></command> | |
| 22 <inputs> | |
| 23 <expand macro="gff3_input" /> | |
| 24 <param label="Blastp Results" name="blast" type="data" format="blastxml"/> | |
| 25 <param label="Separation Minimum" name="minimum" type="text" value="-1" | |
| 26 help="Minimum number of amino acids a CDS pair must be separated by to detect an intron. Set to a negative number to instead allow CDS to overlap by up to that many AAs."/> | |
| 27 <param label="Separation Maximum" name="maximum" type="integer" value="10000" | |
| 28 help="Maximum number of bases a CDS pair may be separated by to detect an intron (eg, distance from end of 1 cds to the start of another)."/> | |
| 29 <param label="Percent Identity Threshold" name="idThresh" type="float" value=".30" | |
| 30 help="Minimum Identity Percentage for HSP to be considered for intron comparison (0.00 to 1.00)"/> | |
| 31 </inputs> | |
| 32 <outputs> | |
| 33 <data format="gff3" name="output" label="Potential interrupted genes"/> | |
| 34 </outputs> | |
| 35 <tests> | |
| 36 <test> | |
| 37 <param name="gff3_data" value="T7_CLEAN.gff3"/> | |
| 38 <param name="blast" value="T7_NR.blastxml"/> | |
| 39 <param name="minimum" value="10" /> | |
| 40 <param name="maximum" value="2000" /> | |
| 41 <param name="idThresh" value="0.3" /> | |
| 42 <output name="output" file="T7_INTRON.gff3"/> | |
| 43 </test> | |
| 44 </tests> | |
| 45 <help><![CDATA[ | |
| 46 **What it does** | |
| 47 | |
| 48 This tool parses BLAST XML results and returns potential intron regions by | |
| 49 identifying query proteins with BLAST hits to the same target protein within | |
| 50 the maximum number of bases set above. This distance will also wraparound the | |
| 51 ends of the genome. The list of hits is returned as a gff3. | |
| 52 | |
| 53 (Tool formerly named Intron Detection, updated Nov 2020) | |
| 54 | |
| 55 ]]></help> | |
| 56 <expand macro="citations-2020" /> | |
| 57 </tool> |