Mercurial > repos > jjohnson > mzsqlite_psm_align

annotate mzsqlite_psm_align.xml @ 6:100cff4db790 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit ae4270ce6b1052d7eaac8e1e816263ad17f3db51-dirty
author jjohnson
date Tue, 10 Apr 2018 11:58:31 -0400
parents af5f22779a8e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
1 <tool id="mzsqlite_psm_align" name="MzSQLite ProBED ProBAM" version="0.1.0">
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
2 <description>from mz.sqlite aand genomic mapping</description>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
3 <requirements>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
4 <requirement type="package">biopython</requirement>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
5 <requirement type="package">twobitreader</requirement>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
6 <requirement type="package">pysam</requirement>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
7 <requirement type="package">gffutils</requirement>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
8 </requirements>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
5
af5f22779a8e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit d65efea03eb2db8a43e64599a4f899ead1a252ba-dirty
jjohnson
parents: 4
diff changeset
10 #if $readlignments:
af5f22779a8e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit d65efea03eb2db8a43e64599a4f899ead1a252ba-dirty
jjohnson
parents: 4
diff changeset
11 ln -s -f '${$readlignments}' 'input.bam' &&
af5f22779a8e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit d65efea03eb2db8a43e64599a4f899ead1a252ba-dirty
jjohnson
parents: 4
diff changeset
12 ln -s -f '${$readlignments.metadata.bam_index}' 'input.bam.bai' &&
af5f22779a8e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit d65efea03eb2db8a43e64599a4f899ead1a252ba-dirty
jjohnson
parents: 4
diff changeset
13 #end if
0
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
14 python '$__tool_directory__/mzsqlite_psm_align.py'
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
15 #if $ref.ref_source == 'cached':
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
16 --twobit='$ref.ref_loc.fields.path'
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
17 #elif $ref.ref_source == 'history':
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
18 --twobit='$ref.ref_file'
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
19 #end if
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
20 #if $gffutilsdb:
6
100cff4db790 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit ae4270ce6b1052d7eaac8e1e816263ad17f3db51-dirty
jjohnson
parents: 5
diff changeset
21 --gffutils_sqlite '$gffutilsdb'
0
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
22 #end if
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
23 #if $readlignments:
5
af5f22779a8e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit d65efea03eb2db8a43e64599a4f899ead1a252ba-dirty
jjohnson
parents: 4
diff changeset
24 --reads_bam 'input.bam'
0
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
25 #end if
3
ce4174c80be5 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 3a37749e711a57ed1ca14b7d23a7ce14f630e6fe-dirty
jjohnson
parents: 2
diff changeset
26 #if 'probed' in str($output_formats).split(','):
0
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
27 --probed '$probed'
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
28 #end if
3
ce4174c80be5 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 3a37749e711a57ed1ca14b7d23a7ce14f630e6fe-dirty
jjohnson
parents: 2
diff changeset
29 #if 'prosam' in str($output_formats).split(','):
0
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
30 --prosam '$prosam'
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
31 #end if
3
ce4174c80be5 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 3a37749e711a57ed1ca14b7d23a7ce14f630e6fe-dirty
jjohnson
parents: 2
diff changeset
32 #if 'probam' in str($output_formats).split(','):
0
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
33 --probam '$probam'
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
34 #end if
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
35 #if $genomicref:
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
36 --genomeReference $genomicref
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
37 #else
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
38 --genomeReference $genomicdb.metadata.dbkey
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
39 #end if
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
40 '$mzsqlitedb' '$genomicdb'
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
41 ]]></command>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
42 <inputs>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
43 <param name="mzsqlitedb" type="data" format="mz.sqlite" label="mz.sqlite databse"/>
2
46113c737b68 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 4c5f3f9b68fca6467a95b5f7f749469e4ab46bf8-dirty
jjohnson
parents: 0
diff changeset
44 <param name="genomicdb" type="data" format="sqlite" label="genomic mapping sqlite databse"/>
0
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
45 <conditional name="ref">
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
46 <param name="ref_source" type="select" label="Source for Genomic Sequence Data">
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
47 <option value="cached">Locally cached twobit</option>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
48 <option value="history">History dataset twobit</option>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
49 </param>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
50 <when value="cached">
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
51 <param name="ref_loc" type="select" label="Select reference 2bit file">
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
52 <options from_data_table="twobit" />
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
53 </param>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
54 </when>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
55 <when value="history">
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
56 <param name="ref_file" type="data" format="twobit" label="reference 2bit file" />
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
57 </when>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
58 </conditional>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
59 <param name="gffutilsdb" type="data" format="sqlite" label="gffutils sqlite database" optional="true"/>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
60 <param name="readlignments" type="data" format="bam" label="read alignments bam" optional="true"/>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
61 <param name="genomicref" type="text" value="" label="Genome Reference name" optional="true"/>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
62 <param name="output_formats" type="select" display="checkboxes" label="outputs" multiple="true">
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
63 <option value="probam">pro.bam</option>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
64 <option value="prosam">pro.sam</option>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
65 <option value="probed">pro.bed</option>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
66 </param>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
67 </inputs>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
68 <outputs>
5
af5f22779a8e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit d65efea03eb2db8a43e64599a4f899ead1a252ba-dirty
jjohnson
parents: 4
diff changeset
69 <data name="prosam" format="sam" label="pro.SAM on ${on_string}">
0
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
70 <filter>'prosam' in output_formats</filter>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
71 </data>
5
af5f22779a8e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit d65efea03eb2db8a43e64599a4f899ead1a252ba-dirty
jjohnson
parents: 4
diff changeset
72 <data name="probam" format="bam" label="pro.Bam on ${on_string}">
0
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
73 <filter>'probam' in output_formats</filter>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
74 </data>
5
af5f22779a8e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit d65efea03eb2db8a43e64599a4f899ead1a252ba-dirty
jjohnson
parents: 4
diff changeset
75 <data name="probed" format="bed" label="pro.Bed on ${on_string}">
0
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
76 <filter>'probed' in output_formats</filter>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
77 </data>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
78 </outputs>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
79 <help><![CDATA[
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
80
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
81 Generates proBAM or proBED feature alignment files for peptides identified from a mass spectrometry protein search analysis.
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
82
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
83 The tool mz_to_sqlite generates the a SQLite database for a mzIdentML file,
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
84 along with the fasta search database and the spectrum files used in the search.
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
85
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
86 The genomic mapping sqlite database has this schema:
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
87
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
88 CREATE TABLE feature_cds_map ( /* One row for each exon in the search protein */
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
89 name TEXT, /* Accession name of search protein in mzIdentML */
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
90 chrom TEXT, /* Reference genome chromosome for this exon */
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
91 start INTEGER, /* genomic start of the exon (zero-based like BED) */
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
92 end INTEGER, /* genomic end of the exon (non-incluse like BED) */
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
93 strand TEXT, /* genomic strand: '+' or '-' */
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
94 cds_start INTEGER, /* The CDS coding start for this exon (zero-based) */
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
95 cds_end INTEGER /* The CDS coding start end this exon (non-inclusive) */
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
96 );
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
97
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
98 Example:
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
99 sqlite> select * from feature_cds_map WHERE name like 'ENSMUSP00000000001%';
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
100 ENSMUSP00000000001 chr3 108145887 108146005 - 0 118
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
101 ENSMUSP00000000001 chr3 108123794 108123837 - 118 161
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
102 ENSMUSP00000000001 chr3 108123541 108123683 - 161 303
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
103 ENSMUSP00000000001 chr3 108118300 108118458 - 303 461
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
104 ENSMUSP00000000001 chr3 108115762 108115891 - 461 590
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
105 ENSMUSP00000000001 chr3 108112472 108112602 - 590 720
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
106 ENSMUSP00000000001 chr3 108111934 108112088 - 720 874
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
107 ENSMUSP00000000001 chr3 108109421 108109612 - 874 1065
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
108
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
109 This schema can describe structural variants as well as canonical transcripts.
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
110
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
111 ]]></help>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
112 </tool>