Mercurial > repos > mvdbeek > damidseq_polii_gene_call

annotate damid_polII_gene_call.xml @ 0:af687b0ddff9 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/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
author mvdbeek
date Fri, 20 Apr 2018 10:25:48 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
1 <tool id="damidseq_polII_gene_call" name="Calculate polII occupancy" version="1.0.2">
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
2 <description>from DamIDseq data</description>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
3 <requirements>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
4 <requirement type="package" version="3.4">R</requirement>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
5 </requirements>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
6 <version_command><![CDATA[Rscript '$__tool_directory__/polii.gene.call' | grep -o "v.*"]]></version_command>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
7 <command detect_errors="aggressive"><![CDATA[
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
8 ln -fs '$genes' genes.gff &&
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
9 ln -fs '$input_file' input.$input_file.ext &&
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
10 Rscript '$__tool_directory__/polii.gene.call' --genes.file=genes.gff input.$input_file.ext --iter=$iter --fdr=$fdr &&
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
11 mv *.details.csv details.csv &&
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
12 mv *.genes genes.csv
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
13 ]]></command>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
14 <inputs>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
15 <param name="input_file" type="data" format="gff,bed,bedgraph" label="Select dam-fusion/dam ratio files" help="You can use damidseq_core to produce this file."/>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
16 <param name="genes" type="data" format="gff" label="Select a GFF file containing genes for which to calculate occupancy"/>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
17 <param name="iter" type="integer" min="1" value="50000" label="Number of iterations for calculation of FDR"/>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
18 <param name="fdr" type="float" min="0" max="1" value="0.01" label="FDR cutoff for gene list"/>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
19 </inputs>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
20 <outputs>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
21 <data name="details" format="csv" from_work_dir="details.csv" label="${tool.name} gene details on ${on_string}"/>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
22 <data name="sig_genes" format="csv" from_work_dir="genes.csv" label="${tool.name} genes on ${on_string}"/>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
23 </outputs>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
24 <tests>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
25 <test>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
26 <param name="input_file" value="polII.bed" ftype="bedgraph"/>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
27 <param name="genes" value="genes.gff" ftype="gff"/>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
28 <param name="fdr" value="1"/>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
29 <param name="iter" value="500"/>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
30 <output name="details" value="details.csv" compare="sim_size"/>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
31 <output name="sig_genes" value="genes.csv" compare="sim_size"/>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
32 </test>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
33 </tests>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
34 <help><![CDATA[
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
35 What it does
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
36 ------------
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
37
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
38 Rscript for calculating average PolII occupancy and FDR for RNA Pol II DamID datasets, based on original algorithms developed by Tony Southall.
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
39 The script processes datafiles in gatc.bedgraph or gatc.gff format, such as those generated by damidseq_pipeline.
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
40
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
41 Differences between RNA pol II DamID and RNAseq
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
42 -----------------------------------------------
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
43 Although both are methods for transcriptional profiling, please be aware that there may be differences between these two methods. In particular, transcript abundancy as assessed through RNAseq will depend on transcript stability, whereas RNA pol II occupancy may provide a better indication of transcription levels.
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
44
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
45
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
46 ]]></help>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
47 <citations>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
48 <citation type="doi">10.1093/bioinformatics/btv386</citation>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
49 </citations>
af687b0ddff9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
50 </tool>