Mercurial > repos > jjohnson > mzsqlite_psm_align

annotate mzsqlite_psm_align.xml @ 0:492f98d89e26 draft

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 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
author jjohnson
date Tue, 10 Apr 2018 09:57:49 -0400
parents
children 46113c737b68
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[
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
10 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
11 #if $ref.ref_source == 'cached':
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
12 --twobit='$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
13 #elif $ref.ref_source == 'history':
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
14 --twobit='$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
15 #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
16 #if $gffutilsdb:
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
17 --gffutils_file '$gffutilsdb'
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
18 #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
19 #if $readlignments:
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
20 --reads_bam '$readlignments'
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
21 #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
22 #if 'probed' in $output_formats:
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
23 --probed '$probed'
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
24 #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
25 #if 'prosam' in $output_formats:
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
26 --prosam '$prosam'
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
27 #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
28 #if 'probam' in $output_formats:
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
29 --probam '$probam'
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
30 #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
31 #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
32 --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
33 #else
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
34 --genomeReference $genomicdb.metadata.dbkey
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
35 #end if
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
36 '$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
37 ]]></command>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
38 <inputs>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
39 <param name="mzsqlitedb" type="data" format="mz.sqlite" label="mz.sqlite databse"/>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
40 <param name="genomicdb" type="data" format="mz.sqlite" label="mz.sqlite databse"/>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
41 <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
42 <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
43 <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
44 <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
45 </param>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
46 <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
47 <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
48 <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
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>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
51 <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
52 <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
53 </when>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
54 </conditional>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
55 <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
56 <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
57 <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
58 <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
59 <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
60 <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
61 <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
62 </param>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
63 </inputs>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
64 <outputs>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
65 <data name="prosam" format="pro.sam">
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
66 <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
67 </data>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
68 <data name="probam" format="pro.bam">
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
69 <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
70 </data>
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 name="probed" format="pro.bed">
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
72 <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
73 </data>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
74 </outputs>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
75 <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
76
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
77 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
78
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
79 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
80 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
81
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
82 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
83
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
84 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
85 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
86 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
87 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
88 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
89 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
90 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
91 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
92 );
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
93
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
94 Example:
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
95 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
96 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
97 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
98 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
99 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
100 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
101 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
102 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
103 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
104
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
105 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
106
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
107 ]]></help>
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
108 </tool>