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