diff megablast_wrapper.xml @ 0:dc7b4acb3fa6 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/megablast_wrapper.xml	Mon May 19 12:33:49 2014 -0400
@@ -0,0 +1,88 @@
+<tool id="megablast_wrapper" name="Megablast" version="1.2.0">
+    <description> compare short reads against htgs, nt, and wgs databases</description>
+    <requirements>
+        <requirement type="package" version="2.2.26+">blast+</requirement>
+        <requirement type="package" version="0.7.1">bx-python</requirement>
+    </requirements>
+    <command interpreter="python">
+      megablast_wrapper.py
+        --db_build="${source_select.fields.path}"
+        --input=$input_query
+        --word_size=$word_size
+        --identity_cutoff=$iden_cutoff
+        --eval_cutoff=$evalue_cutoff 
+        --filter_query=$filter_query
+        --index_dir=${GALAXY_DATA_INDEX_DIR}
+        --output=$output1
+    </command>
+    <inputs>
+        <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_data_table="blastdb" />
+        </param>
+        <param name="word_size" type="select" label="using word size" help="Size of best perfect match (-word_size)">
+            <option value="28">28</option>
+            <option value="16">16</option>
+        </param>
+        <param name="iden_cutoff" type="float" size="15" value="90.0" label="report hits above this identity (-perc_identity)" help="no cutoff if 0" />
+        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff (-evalue)" />
+        <param name="filter_query" type="select" label="Filter out low complexity regions? (-dust)">
+            <option value="yes">Yes</option>
+            <option value="no">No</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output1" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/>
+            <!-- source_select needs to match the entry in the blastdb.loc file, which includes the last update date if appropriate --> 
+            <param name="source_select" value="phiX" />
+            <param name="word_size" value="28" />
+            <param name="iden_cutoff" value="99.0" />
+            <param name="evalue_cutoff" value="10.0" />
+            <param name="filter_query" value="yes" />
+            <output name="output1" file="megablast_wrapper_test1.out"/> 
+        </test>
+    </tests>
+    <help>
+    
+.. class:: warningmark
+
+**Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing.  
+
+-----
+
+**What it does**
+
+This tool runs **megablast** function of BLAST+ blastn tool - a high performance nucleotide local aligner developed by Webb Miller and colleagues.
+
+-----
+
+**Output format**
+
+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**
+
+Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214.
+
+    </help>
+</tool>