Mercurial > repos > bgruening > diamond

annotate macros.xml @ 12:60f307965815 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
author iuc
date Mon, 03 Feb 2025 16:01:01 +0000
parents 1e3323a44643
children 20d92dc4c6cb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff changeset
1 <macros>
12
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
2 <token name="@TOOL_VERSION@">2.1.11</token>
10
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
iuc
parents: 9
diff changeset
3 <token name="@VERSION_SUFFIX@">0</token>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff changeset
4 <xml name="requirements">
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff changeset
5 <requirements>
12
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
6 <requirement type="package" version="@TOOL_VERSION@">diamond</requirement>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff changeset
7 </requirements>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff changeset
8 </xml>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff changeset
9 <xml name="stdio">
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff changeset
10 <stdio>
12
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
11 <regex match="Failed to allocate" source="stderr" level="fatal_oom"/>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff changeset
12 </stdio>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff changeset
13 </xml>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff changeset
14 <xml name="version_command">
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
15 <version_command>diamond version | cut -d" " -f 3</version_command>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff changeset
16 </xml>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
17 <xml name="output_type_macro">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
18 <conditional name="output">
10
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
iuc
parents: 9
diff changeset
19 <param argument="--outfmt" type="select" label="Format of output file" help="">
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
20 <option value="0">BLAST pairwise</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
21 <option value="5">BLAST XML</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
22 <option value="6">BLAST tabular</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
23 <option value="100">DAA</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
24 <option value="101">SAM</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
25 <option value="102">Taxonomic classification</option>
12
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
26 <option value="104">JSON (flat)</option>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
27 </param>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
28 <when value="0"/>
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
29 <when value="5"/>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
30 <when value="6">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
31 <param name="fields" type="select" label="Tabular fields" help="" multiple="true">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
32 <option value="qseqid" selected="true">Query Seq - id</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
33 <option value="sseqid" selected="true">Subject Seq - id</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
34 <option value="sallseqid">All subject Seq - id(s)</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
35 <option value="qlen">Query sequence length</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
36 <option value="slen">Subject sequence length</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
37 <option value="pident" selected="true">Percentage of identical matches</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
38 <option value="length" selected="true">Alignment length</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
39 <option value="nident">Number of identical matches</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
40 <option value="mismatch" selected="true">Number of mismatches</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
41 <option value="positive">Number of positive - scoring matches</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
42 <option value="gapopen" selected="true">Number of gap openings</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
43 <option value="gaps">Total number of gaps</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
44 <option value="ppos">Percentage of positive - scoring matches</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
45 <option value="qstart" selected="true">Start of alignment in query</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
46 <option value="qend" selected="true">End of alignment in query</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
47 <option value="sstart" selected="true">Start of alignment in subject</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
48 <option value="send" selected="true">End of alignment in subject</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
49 <option value="qseq">Aligned part of query sequence</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
50 <option value="sseq">Aligned part of subject sequence</option>
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
51 <option value="qseq_translated">Translation of the aligned part of query sequence</option>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
52 <option value="evalue" selected="true">Expect value</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
53 <option value="bitscore" selected="true">Bit score</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
54 <option value="score">Raw score</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
55 <option value="qframe">Query frame</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
56 <option value="btop">Blast traceback operations(BTOP)</option>
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
57 <option value="scovhsp">Subject coverage per HSP</option>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
58 <option value="stitle">Subject Title</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
59 <option value="salltitles">All Subject Title(s)</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
60 <option value="qcovhsp">Query Coverage Per HSP</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
61 <option value="qtitle">Query title</option>
7
62c9df8382c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents: 6
diff changeset
62 <option value="full_qseq">Query sequence</option>
62c9df8382c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents: 6
diff changeset
63 <option value="full_sseq">Subject sequence</option>
62c9df8382c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents: 6
diff changeset
64 <option value="qqual">Query quality values for the aligned part of the query</option>
62c9df8382c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents: 6
diff changeset
65 <option value="full_qqual">Query quality values</option>
62c9df8382c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
bgruening
parents: 6
diff changeset
66 <option value="qstrand">Query strand</option>
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
67 <option value="cigar">Cigar</option>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
68 <yield/>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
69 </param>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
70 </when>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
71 <when value="100">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
72 </when>
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
73 <when value="101">
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
74 </when>
12
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
75 <when value="102">
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
76 <param argument="--include-lineage" type="boolean" truevalue="--include-lineage" falsevalue="" checked="false" label="Include lineage in the taxonomic classification format"/>
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
77 </when>
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
78 <when value="104"/>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
79 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
80 </xml>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
81 <xml name="hit_filter_macro">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
82 <conditional name="hit_filter">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
83 <param name="hit_filter_select" type="select" label="Method to restrict the number of hits?">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
84 <option value="max">Maximum number of target sequences</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
85 <option value="top">Percentage of top alignment score</option>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
86 </param>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
87 <when value="max">
12
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
88 <param argument="--max-target-seqs" type="integer" value="25" label="The maximum number of target sequences per query to report alignments for" help="Setting this to 0 will report all alignments that were found."/>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
89 </when>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
90 <when value="top">
12
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
91 <param argument="--top" type="integer" value="0" label="Keep alignments within the given percentage range of the top alignment score for a query" help="For example, setting this to 10 will report all alignments whose score is at most 10% lower than the best alignment score for a query."/>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
92 </when>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
93 </conditional>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
94 </xml>
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
95 <xml name="block_size_low_sens">
12
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
96 <param argument="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time"
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
97 help="This is the main parameter for controlling the program’s memory and disk space usage. Bigger numbers will increase the use of memory and temporary disk space, but also improve performance"/>
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
98 </xml>
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
99 <xml name="block_size_hi_sens">
12
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
100 <param argument="--block-size" type="float" value="0.4" label="Block size in billions of sequence letters to be processed at a time"
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
101 help="This is the main parameter for controlling the program’s memory and disk space usage. Bigger numbers will increase the use of memory and temporary disk space, but also improve performance"/>
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
102 </xml>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff changeset
103 <xml name="citations">
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff changeset
104 <citations>
12
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
105 <citation type="doi">10.1038/s41592-021-01101-x</citation>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff changeset
106 </citations>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff changeset
107 </xml>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
108 <xml name="output_macro">
12
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
109 <data format="txt" name="blast_pairw" label="${tool.name} on ${on_string}: Blast pairwise">
10
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
iuc
parents: 9
diff changeset
110 <filter>output_section["output"]["outfmt"] == "0"</filter>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
111 </data>
12
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
112 <data format="xml" name="blast_xml" label="${tool.name} on ${on_string}: Blast XML">
10
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
iuc
parents: 9
diff changeset
113 <filter>output_section["output"]["outfmt"] == "5"</filter>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
114 </data>
12
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
115 <data format="tabular" name="blast_tabular" label="${tool.name} on ${on_string}: Blast Tabular">
10
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
iuc
parents: 9
diff changeset
116 <filter>output_section["output"]["outfmt"] == "6"</filter>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
117 </data>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
118 <!-- for daa diamond appends the .daa extension -> hence from_work_dir -->
12
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
119 <data format="daa" name="daa_output" label="${tool.name} on ${on_string}: DAA" from_work_dir="output.daa">
10
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
iuc
parents: 9
diff changeset
120 <filter>output_section["output"]["outfmt"] == "100"</filter>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
121 </data>
12
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
122 <data format="sam" name="sam_output" label="${tool.name} on ${on_string}: SAM">
10
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
iuc
parents: 9
diff changeset
123 <filter>output_section["output"]["outfmt"] == "101"</filter>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
124 </data>
12
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
125 <data format="tabular" name="tax_output" label="${tool.name} on ${on_string}: Taxonomic classification">
10
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
iuc
parents: 9
diff changeset
126 <filter>output_section["output"]["outfmt"] == "102"</filter>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
127 </data>
12
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
128 <data format="json" name="json_output" label="${tool.name} on ${on_string}: Json flat">
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
129 <filter>output_section["output"]["outfmt"] == "104"</filter>
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
130 </data>
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
131 </xml>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
132 <token name="@OUTPUT_ARGS@">
10
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
iuc
parents: 9
diff changeset
133 #if $output_section.output.outfmt == "0"
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
134 --outfmt '0'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
135 --out '$blast_pairw'
10
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
iuc
parents: 9
diff changeset
136 #else if $output_section.output.outfmt == "5"
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
137 --outfmt '5'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
138 --out '$blast_xml'
10
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
iuc
parents: 9
diff changeset
139 #else if $output_section.output.outfmt == "6"
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
iuc
parents: 9
diff changeset
140 --outfmt '6' #echo ' '.join(str($output_section.output.fields).split(','))
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
141 --out '$blast_tabular'
10
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
iuc
parents: 9
diff changeset
142 #else if $output_section.output.outfmt == "100"
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
143 --outfmt '100'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
144 --out output.daa
10
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
iuc
parents: 9
diff changeset
145 #else if $output_section.output.outfmt == "101"
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
146 --outfmt '101'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
147 --out '$sam_output'
10
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
iuc
parents: 9
diff changeset
148 #else if $output_section.output.outfmt == "102"
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
149 --outfmt '102'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
150 --out '$tax_output'
12
60f307965815 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
iuc
parents: 10
diff changeset
151 $output_section.output.include_lineage
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
152 #end if
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
153 </token>
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
154 <token name="@HITFILTER_ARGS@">
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
155 #if str($hit_filter.hit_filter_select) == 'max':
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
156 --max-target-seqs '$hit_filter.max_target_seqs'
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
157 #else:
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
158 --top '$hit_filter.top'
8
54f751e413f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
iuc
parents: 7
diff changeset
159 #end if
6
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents: 1
diff changeset
160 </token>
1
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff changeset
161 </macros>