diff Iterative_mapping/iterative_map.xml @ 66:d2817a631a7b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Iterative_mapping/iterative_map.xml	Tue Nov 18 16:24:04 2014 -0500
@@ -0,0 +1,96 @@
+<tool id="iterative_map_pipeline" name="Iterative Mapping" version="1.0">
+	<description></description>
+	<command interpreter="python">
+        #if $mapping_file.type == "user"
+            iterative_map.py $file_format.type $file_format.seq_file $reference_file $shift $length $t_end $mapping_file.type $output $mapping_file.param_v $mapping_file.param_five $mapping_file.param_three $mapping_file.param_k $mapping_file.param_a $mapping_file.param_m $mapping_file.param_best  
+        #else
+            iterative_map.py $file_format.type $file_format.seq_file $reference_file $shift $length $t_end $mapping_file.type $output
+        #end if
+    </command>
+        <requirements>
+                <requirement type="package" version="1.61">biopython</requirement>
+                <requirement type="package" version="1.7.1">numpy</requirement>
+                <requirement type="package" version="0.1.18">samtools</requirement>
+                <requirement type="package" version="0.12.7">bowtie</requirement>
+        </requirements>
+	<inputs>
+                <conditional name="file_format">
+                  <param name="type" type="select" label="File format of the reads (Default FASTQ)">
+                    <option value="fastq">FASTQ</option>
+                    <option value="fasta">FASTA</option>
+                  </param>
+                  <when value="fastq">
+                    <param name="seq_file" type="data" format="fastq" label="Fastq file"/>
+                  </when>
+                  <when value="fasta">
+                    <param name="seq_file" type="data" format="fasta" label="Fasta file"/>
+                  </when>
+                </conditional>
+		        <param name="reference_file" type="data" format="fasta" label="Reference genome/transcriptome"/>
+                <param name="shift" type="integer" value="1" label="Number of nucleotides trimmed each round"/>
+                <param name="length" type="integer" value="21" label="Minimum requirement of read length for mapping"/>
+                <param name="t_end" type="select" label="Trim from 5' or 3' end">
+                    <option value="five_end">5' end</option>
+                    <option value="three_end">3' end</option>
+                </param>
+                
+                <conditional name="mapping_file">
+                  <param name="type" type="select" label="Bowtie mapping flags (Default -v 0 -a --best --strata)">
+                    <option value="default">Default</option>
+                    <option value="user">User specified</option>
+                  </param>
+                  <when value="default"/>
+                  <when value="user"> 
+                    <param name="param_v" type="integer" value="0" label="Number of mismatches for SOAP-like alignment policy (-v)"/>
+                    <param name="param_five" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)"/>
+                    <param name="param_three" type="integer" value="0" label="Trim n bases from high-quality (right) end of each read before alignment (-3)"/>
+                    <param name="param_k" type="integer" value="1" label="Report up to n valid alignments per read (-k)"/>
+                    <param name="param_a" type="boolean" checked="False" truevalue = "1" falsevalue = "0" label="Whether or not to report all valid alignments per read (-a)"/>
+                    <param name="param_m" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m), -1 for unlimited"/>
+                    <param name="param_best" type="boolean" checked="False" truevalue = "1" falsevalue = "0" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best --strata)"/>
+                  </when>
+                </conditional>
+
+	</inputs>
+	<outputs>
+		<data name="output" type="data" format="bam"/>
+	</outputs>
+    <tests>
+        <test>
+            <param name="file_format.type" value="fasta" />
+            <param name="file_format.seq_file" value="sample.fasta" />
+	        <param name="reference_file" value="rRNA.txt" />
+            <param name="shift" value="1" />
+            <param name="length" value="21" />
+            <param name="mapping_file.type" value="default" />
+	        <output name="output" file="mapped.out" />
+        </test>
+    </tests>
+
+	<help>
+
+
+**TIPS**:
+
+-----
+
+**Input**:
+
+* 1. Sequence file type (FASTA/FASTQ)
+* 2. Sequence file (fasta/fastq format)
+* 3. Reference file (fasta) used to map the reads to
+* 4. “Shift” (The length of the sequence that will be trimmed at the 3’end of the reads before each round of mapping)
+* 5. “Length” (The minimum length of the reads for mapping after trimming)
+* [Optional]
+* 1. Bowtie mapping flags (options) [Default: -v 0 -a --best --strata] (-v flag indicates the number of allowed mismatches. Use -5/-3 flag to trim the nucleotides from 5'/3' end of the reads)
+
+-----
+
+**Output**:
+
+A bam file with all of the reads that are mapped	
+
+
+
+	</help>
+</tool>