Mercurial > repos > galaxyp > sixgill
annotate sixgill_filter.xml @ 0:cf8eee8343fb draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
author | galaxyp |
---|---|
date | Thu, 13 Oct 2016 08:38:04 -0400 |
parents | |
children |
rev | line source |
---|---|
0
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
1 <tool id="sixgill_filter" name="sixgill filter" version="@VERSION@.0"> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
2 <description>a metapeptide database</description> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
3 <macros> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
4 <import>macros.xml</import> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
5 </macros> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
6 <expand macro="requirements" /> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
7 <expand macro="stdio" /> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
8 <version_command>sixgill_filter --version</version_command> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
9 <command><![CDATA[ |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
10 sixgill_filter |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
11 --nogzipout |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
12 --out=metapeptides_db_output.tsv |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
13 #if str($minorflength) != '': |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
14 --minorflength=$minorflength |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
15 #end if |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
16 #if str($minaaseqlength) != '': |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
17 --minaaseqlength=$minaaseqlength |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
18 #end if |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
19 #if str($minqualscore) != '': |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
20 --minqualscore=$minqualscore |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
21 #end if |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
22 #if str($minlongesttryppeplen) != '': |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
23 --minlongesttryppeplen=$minlongesttryppeplen |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
24 #end if |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
25 #if str($minreadcount) != '': |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
26 --minreadcount=$minreadcount |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
27 #end if |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
28 #if str($maxmetapeptides) != '': |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
29 --maxmetapeptides=$maxmetapeptides |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
30 #end if |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
31 $metapeptide_db |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
32 #if 'fa' in str($output_choice): |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
33 && sixgill_makefasta --type=aa --out="metapeptides_fa_output.fa" "metapeptides_db_output.tsv" |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
34 #end if |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
35 ]]></command> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
36 <inputs> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
37 <param name="metapeptide_db" type="data" format="tabular" label="metapeptide database" |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
38 help="Can be generated with sixgill_build"/> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
39 <param name="minorflength" type="integer" value="40" min="0" optional="true" label="minorflength" |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
40 help="min length of ORF-portion"/> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
41 <param name="minaaseqlength" type="integer" value="10" min="0" optional="true" label="minaaseqlength" |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
42 help="min AA sequence length"/> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
43 <param name="minqualscore" type="integer" value="30" min="0" optional="true" label="minqualscore" |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
44 help="min base-call phred score across any NT in a metapeptide"/> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
45 <param name="minlongesttryppeplen" type="integer" value="7" min="0" optional="true" label="minlongesttryppeplen" |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
46 help="minimum length of the longest tryptic peptide"/> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
47 <param name="minreadcount" type="integer" value="2" min="1" optional="true" label="minreadcount" |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
48 help="minimum read count"/> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
49 <param name="minmetagenescore" type="integer" value="" min="-1" optional="true" label="minmetagenescore" |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
50 help="minimum MetaGene score"/> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
51 <param name="maxmetapeptides" type="integer" value="" optional="true" label="maxmetapeptides" |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
52 help="maximum number of metapeptides to write"/> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
53 <param name="output_choice" type="select" multiple="true" optional="false" label="select outputs"> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
54 <option value="db" selected="true">metapeptide database</option> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
55 <option value="fa">metapeptide protein fasta</option> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
56 </param> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
57 </inputs> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
58 <outputs> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
59 <data name="output_db" format="tabular" label="${tool.name} on ${on_string}: metapeptides.tsv" from_work_dir="metapeptides_db_output.tsv"> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
60 <filter>'db' in output_choice</filter> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
61 <actions> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
62 <action name="comment_lines" type="metadata" default="1" /> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
63 <action name="column_names" type="metadata" default="sequence,length,min_qualscore,partial_orf_length,metagene_score,read_ids" /> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
64 </actions> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
65 </data> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
66 <data name="output_fa" format="fasta" label="${tool.name} on ${on_string}: metapeptides.fa" from_work_dir="metapeptides_fa_output.fa"> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
67 <filter>'fa' in output_choice</filter> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
68 </data> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
69 </outputs> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
70 <tests> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
71 <test> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
72 <param name="metapeptide_db" ftype="tabular" value="metagene_nometagene_merged.metapeptides.tsv"/> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
73 <param name="minreadcount" value="2"/> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
74 <param name="minaaseqlength" value="12"/> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
75 <param name="output_choice" value="db"/> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
76 <output name="output_db"> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
77 <assert_contents> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
78 <has_text text="DLRILLRERLVAGDSDEAAVDFIVDR" /> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
79 <not_has_text text="YHNFEGYRWR" /> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
80 </assert_contents> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
81 </output> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
82 </test> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
83 </tests> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
84 <help><![CDATA[ |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
85 usage: sixgill_filter [-h] --out OUT [--minorflength MINORFLENGTH] |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
86 [--minaaseqlength MINAASEQLENGTH] |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
87 [--minreadcount MINREADCOUNT] |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
88 [--minqualscore MINQUALSCORE] |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
89 [--minlongesttryppeplen MINLONGESTTRYPPEPLEN] |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
90 [--minmetagenescore MINMETAGENESCORE] |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
91 [--maxmetapeptides MAXMETAPEPTIDES] [--debug] |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
92 metapeptidefile |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
93 |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
94 Filter a metapeptide database. |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
95 |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
96 positional arguments: |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
97 metapeptidefile input metapeptide database file |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
98 |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
99 optional arguments: |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
100 -h, --help show this help message and exit |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
101 --out OUT output metapeptide database file |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
102 --minorflength MINORFLENGTH |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
103 minimum ORF length |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
104 --minaaseqlength MINAASEQLENGTH |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
105 minimum AA sequence length |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
106 --minreadcount MINREADCOUNT |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
107 minimum read count |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
108 --minqualscore MINQUALSCORE |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
109 minimum basecall quality |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
110 --minlongesttryppeplen MINLONGESTTRYPPEPLEN |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
111 minimum length of the longest tryptic peptide |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
112 --minmetagenescore MINMETAGENESCORE |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
113 Minimum MetaGene score (-1 for none) |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
114 --maxmetapeptides MAXMETAPEPTIDES |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
115 maximum number of metapeptides to write |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
116 --debug Enable debug logging |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
117 |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
118 ]]></help> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
119 <expand macro="citations" /> |
cf8eee8343fb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
galaxyp
parents:
diff
changeset
|
120 </tool> |