ceas: data_manager/data_manager_ceas_fetch

annotate data_manager/data_manager_ceas_fetch_annotations.xml @ 9:4c3b7130dbbb draft

Bump version to 1.0.2-3 to reflect dependency updates.

author	pjbriggs
date	Tue, 18 Oct 2016 09:24:30 -0400
parents	4e2883bb058d
children	b5d686bb9d6f

rev	line source
1 d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	1 <tool id="data_manager_fetch_ceas_annotations" name="Fetch CEAS annotation" version="0.0.1" tool_type="manage_data">
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	2 <requirements>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	3 <requirement type="package" version="1.2.5">python_mysqldb</requirement>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	4 <requirement type="package" version="0.7.1">bx_python</requirement>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	5 <requirement type="package" version="1.0.2.d8c0751">cistrome_ceas</requirement>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	6 </requirements>
1 d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	7 <description>Fetch and install annotation databases for CEAS</description>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	8 <command interpreter="python">data_manager_ceas_fetch_annotations.py
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	9 "${out_file}"
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	10 "${description}"</command>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	11 <inputs>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	12 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	13 <param type="text" name="unique_id" label="Internal identifier"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	14 help="Identifier string to associate with the annotation e.g. 'mm9_generic'" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	15 <param type="text" name="description" value="" size="50"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	16 label="Description of annotation"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	17 help="Text that will be displayed to the user when selecting which annotation to use" />
1 d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	18 <conditional name="reference_source">
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	19 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	20 <option value="web" selected="True">CEAS website</option>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	21 <option value="server">File on the server</option>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	22 <option value="from_wig">Generated from wig file</option>
1 d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	23 </param>
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	24 <when value="web">
1 d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	25 <param type="select" name="annotation_url">
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	26 <option value="http://liulab.dfci.harvard.edu/CEAS/src/hg18.refGene.gz">hg18</option>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	27 <option value="http://liulab.dfci.harvard.edu/CEAS/src/hg19.refGene.gz">hg19</option>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	28 <option value="http://liulab.dfci.harvard.edu/CEAS/src/mm8.refGene.gz">mm8</option>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	29 <option value="http://liulab.dfci.harvard.edu/CEAS/src/mm9.refGene.gz">mm9</option>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	30 <option value="http://liulab.dfci.harvard.edu/CEAS/src/dm2.refGene.gz">dm2</option>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	31 <option value="http://liulab.dfci.harvard.edu/CEAS/src/dm3.refGene.gz">dm3</option>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	32 <option value="http://liulab.dfci.harvard.edu/CEAS/src/ce4.refGene.gz">ce4</option>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	33 <option value="http://liulab.dfci.harvard.edu/CEAS/src/ce6.refGene.gz">ce6</option>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	34 </param>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	35 </when>
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	36 <when value="server">
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	37 <param type="text" name="annotation_filename" value="" size="50"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	38 label="Full path to CEAS annotation table file on disk" optional="False" />
1 d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	39 <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to orignal data instead of copying" checked="False" />
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	40 </when>
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	41 <when value="from_wig">
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	42 <param type="data" format="wig" name="wig_file" value=""
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	43 label="Wig file to use for the background genome annotation"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	44 help="Will be used as input to build_genomeBG" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	45 <param type="select" name="gene_annotation"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	46 label="Gene annotation from UCSC">
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	47 <option value="refGene">refGene</option>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	48 </param>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	49 </when>
1 d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	50 </conditional>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	51 </inputs>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	52 <outputs>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	53 <data name="out_file" format="data_manager_json"/>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	54 </outputs>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	55 <tests>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	56 <test>
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	57 <!-- No tests defined, yet -->
1 d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	58 </test>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	59 </tests>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	60 <help>
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	61
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	62 .. class:: infomark
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	63
1 d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	64 What it does
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	65
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	66 Adds a CEAS gene annotation table file to the ceas_annotations" data table. The
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	67 database file can be downloaded from the CEAS website, imported from a file on the
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	68 Galaxy server, or generated from a ``wig`` file in a Galaxy history.
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	69
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	70 Notice: If you leave the identifier or description blank then they will be
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	71 generated automatically.
1 d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	72
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	73 ------
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	74
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	75 .. class:: infomark
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	76
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	77 Fetching, uploading or creating gene annotation table files
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	78
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	79 The gene annotation table files are SQLite database files which are on the CEAS website:
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	80
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	81 - http://liulab.dfci.harvard.edu/CEAS/usermanual.html
1 d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	82
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	83 The data manager allows you to fetch a pre-built table from the CEAS website; note
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	84 that these are based on the ``RefSeq`` annotation and are only available for a subset
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	85 of genome builds.
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	86
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	87 To create an annotation table for a different genome build or a different annotation,
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	88 use the Generated from wig file option. This runs the CEAS utility ``build_genomeBG``
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	89 to make a custom table from a wig file, which represents the genome background (e.g.
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	90 a wig file created from the ``control lambda`` bedgraph file output from MACS2).
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	91
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	92 Alternatively if you already have an existing custom annotation file then this can be
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 1 diff changeset	93 imported from a path on the Galaxy server.
1 d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	94 </help>
d9032bb158b9 Add in data manager for CEAS annotation databases. pjbriggs parents: diff changeset	95 </tool>

Mercurial > repos > pjbriggs > ceas

annotate data_manager/data_manager_ceas_fetch_annotations.xml @ 9:4c3b7130dbbb draft