annotate galaxy-conf/BaseAlignCounts.xml @ 25:b43c420a6135 draft default tip

Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
author timpalpant
date Sat, 09 Feb 2019 14:02:24 -0500
parents 9d56b5b85740
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
20
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
1 <tool id="BaseAlignCounts" name="Calculate coverage" version="2.0.0">
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
2 <description>of sequencing reads</description>
25
b43c420a6135 Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
timpalpant
parents: 20
diff changeset
3 <command interpreter="bash">galaxyToolRunner.sh ngs.BaseAlignCounts -i $input -a ${chromInfo} -x $X -o $output</command>
20
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
4 <inputs>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
5 <param name="input" type="data" format="sam,bam,bed,bedgraph" label="Sequencing reads" />
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
6 <param name="X" type="integer" value="-1" label="In silico extension (-1 for fragment length)" />
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
7 </inputs>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
8 <outputs>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
9 <data name="output" format="wig" />
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
10 </outputs>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
11 <tests>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
12 </tests>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
13 <help>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
14
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
15 This tool produces a new Wig file with the number of reads/intervals overlapping each base pair. Reads can be artificially extended to match known fragment lengths. If you wish to count the number of reads starting at each base pair, set the read extension to 1. If you wish to count the number of intervals overlapping each base pair, set the extension to -1.
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
16
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
17 -----
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
18
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
19 .. class:: warningmark
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
20
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
21 This tool requires sequencing reads in SAM, BAM, Bed, or BedGraph format. If you are artificially extending reads, ensure that the strand is set correctly in SAM, BAM, and Bed files.
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
22
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
23 .. class:: warningmark
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
24
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
25 Paired-end reads are considered to be the entire fragment (the distance from the 5' end of mate 1 to the 5' end of mate 2) if the extension is set to -1.
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
26
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
27 .. class:: infomark
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
28
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
29 If you would like to convert valued interval data (e.g. BedGraph files from microarrays) to Wig format, use the Converters -> Interval to Wig converter.
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
30
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
31 .. class:: infomark
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
32
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
33 **TIP:** If you are going to be using reads in SAM format for multiple analyses, it is often more efficient to first convert it into BAM format using NGS: SAM Tools -> SAM-to-BAM.
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
34
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
35 -----
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
36
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
37 **Syntax**
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
38
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
39 - **Sequencing reads** are mapped reads from a high-throughput sequencing experiment.
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
40 - **In silico extension:** Reads will be artificially extended from their 5' end to be this length.
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
41
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
42 </help>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
43 </tool>