opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Added column info to MB wrapper

Browse Source
This commit is contained in:
Anton Nekrutenko
2009-04-24 15:06:51 -04:00
parent 186c27814b
commit 871dfe4a6d
2 changed files with 23 additions and 13 deletions
Download Patch File Download Diff File Expand all files Collapse all files
static/welcome.html
+1
View File
@@ -14,6 +14,7 @@
.current-quickie {
width: 100%;
background: black;
borderRadius:10;
}
.quickie .head {
font-size: 200%;
tools/metag_tools/megablast_wrapper.xml
+22 -13
View File
@@ -2,20 +2,20 @@
<description> compare short reads against nt and wgs databases</description>
<command interpreter="python">megablast_wrapper.py $source_select $input_query $output1 $word_size $iden_cutoff $evalue_cutoff $filter_query ${GALAXY_DATA_INDEX_DIR}</command>
<inputs>
<param name="source_select" type="select" display="radio" label="Choose target database">
<param name="input_query" type="data" format="fasta" label="Compare these sequences"/>
<param name="source_select" type="select" display="radio" label="against target database">
<options from_file="blastdb.loc">
<column name="name" index="0"/>
<column name="value" index="0"/>
</options>
</param>
<param name="input_query" type="data" format="fasta" label="Sequence file"/>
<param name="word_size" type="select" label="Word size (-W)" help="Size of best perfect match">
<param name="word_size" type="select" label="using word size" help="Size of best perfect match">
<option value="28">28</option>
<option value="16">16</option>
</param>
<param name="iden_cutoff" type="float" size="15" value="90.0" label="Identity percentage cut-off (-p)" help="no cutoff if 0" />
<param name="evalue_cutoff" type="float" size="15" value="0.001" label="Expectation value (-e)" />
<param name="filter_query" type="select" label="Filter query sequence (-F)">
<param name="iden_cutoff" type="float" size="15" value="90.0" label="report hits above this identity" help="no cutoff if 0" />
<param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" />
<param name="filter_query" type="select" label="Filter out low complexity regions?">
<option value="T">Yes</option>
<option value="F">No</option>
</param>
@@ -49,18 +49,27 @@
This tool runs **megablast** (for information about megablast, please see the reference below) a high performance nucleotide local aligner developed by Webb Miller and colleagues.
-----
**Parameters**
**Output format**
- *Word size* (**-W**) : the minimal length of an exact match
- *Identity percentage cut-off* (**-p**) : the minimal identity for an alignment
- *Expectation value* (**-e**) : the maximal expectation value for an alignment
- *Filter query sequence* (**-F**) : mask low-complexity regions in the query sequence
Output of this tool contains 13 columns delimited by Tabs:
1. Id of your sequence
2. GI of the database hit
3. Length of the database hit
4. % identity
5. Alignment length
6. # mismatches
7. # gaps
8. Start position in your sequence
9. End position in your sequence
10. Start position in database hit
11. End position in database hit
12. E-value
13. Bit score
-----
-------
**Reference**