diff microRNA_pipeline.xml @ 0:87fe81de0931 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/microRNA_pipeline.xml	Sun Jan 04 02:47:25 2015 -0500
@@ -0,0 +1,192 @@
+<tool id="plant_microRNA_v1" name="microRNA_pipeline" veision="1.0.0">
+  <description>Program for plant microRNA analysis (rawdata preprocess -> genome mapping -> non-coding RNA(exclude miRNAs) annotation -> microRNA analysis)</description>
+
+  <requirements>
+	<requirement type="package" version="0.0.13">fastx_toolkit </requirement>
+    <requirement type="package" version="0.12.7">bowtie</requirement>
+    <requirement type="set_environment">SCRIPT_PATH</requirement>
+    <!--requirement type="package" version="3.0.1">R</requirement!-->
+	<requirement type="package" version="1.96">threads</requirement>
+	<requirement type="package" version="2.59">SVG</requirement>
+	<!--requirement type="package" version="0.228">parent</requirement-->
+	<requirement type="package" version="2.1.8">ViennaRNA</requirement>
+  </requirements>
+
+  <!--command interpreter="perl">miPlant.pl -i $input -format $format -gfa $gfa -idx $index -pre $pre -mat $mat -rfam $rfam -idx2 $idx2 -D $D -a $a -M $M -min $min -max $max -mis $mis -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe -t $t -o $output</command-->
+
+  <command interpreter="perl">microRNA_pipeline.pl 
+   ## Change this to accommodate the number of threads you have available.
+        -t \${GALAXY_SLOTS:-4}
+	-path \$SCRIPT_PATH
+
+    #for $j, $s in enumerate( $series )
+    ##rank_of_series=$j
+    -i ${s.input}
+    -tag ${s.tag}
+    #end for
+
+      ## prepare bowtie index
+      #set index_path = ''
+      #if str($reference_genome.source) == "history":
+          #####bowtie-build "$reference_genome.own_file" genome; ln -s "$reference_genome.own_file" genome.fa;
+          #set index_path = $reference_genome.own_file
+		  -gfa $index_path 
+	  #else:
+          #set index_path = $reference_genome.index.fields.path
+		  -gfa ${index_path}.fa -idx $index_path 
+      #end if
+
+
+   ## Do or not annotate rfam non-miRNA RNAs
+    #if $params.annotate_rfam == "yes":
+
+		  ## prepare Rfam bowtie index
+		  #set rfam_index_path = ''
+		  #if str($params.reference_rfam.source) == "history":
+			 ######## bowtie-build "$params.reference_rfam.own_file" rfam; ln -s "$params.reference_rfam.own_file" rfam.fa;
+			  #set rfam_index_path = $params.reference_rfam.own_file
+			 -rfam $rfam_index_path 
+		  #else:
+			#set rfam_index_path = $params.reference_rfam.index.fields.path
+			-rfam ${rfam_index_path}.fa -idx2 $rfam_index_path 
+		  #end if
+
+		-v $params.v 
+	   ## Do or not delete rfam mapped tags
+		#if $params.delete_rfam == "yes":
+		-D 
+		#end if
+	#end if
+
+
+   ## Do or not annotate known microRNAs
+    #if $mirbase.known_microRNA == "yes":
+	-pre $mirbase.pre -mat $mirbase.mat 
+	#end if
+
+
+    -format $format -phred $phred   -a $a -M $mapnt -min $min -max $max -mis $mismatch -e $e -f $f -r $r -dis $dis -flank $flank -mfe $mfe > run.log
+  </command>
+
+  <inputs>
+
+   <repeat name="series" title="Raw sequence data">
+     <param name="input" type="data" label="Raw data"/>
+     <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/>
+   </repeat>
+
+	<param name="format" type="select" label="Raw data format" multiple="false">
+	  <option value="fastq">Raw data is fastq. format</option>
+	  <option value="fasta">Raw data is fasta. format</option>
+	</param>
+
+	<param name="phred" type="select" label="Input quals are Phred+64 or Phred+33" multiple="false">
+	  <option value="64">Phred+64</option>
+	  <option value="33" selected="true">Phred+33</option>
+	</param>
+
+        <conditional name="reference_genome">
+          <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
+            <option value="indexed">Use a built-in index</option>
+            <option value="history">Use one from the history</option>
+          </param>
+          <when value="indexed">
+            <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
+              <options from_data_table="bowtie_indexes">
+                <filter type="sort_by" column="2"/>
+                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
+              </options>
+            </param>
+          </when>
+          <when value="history">
+            <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
+          </when>
+        </conditional>
+
+	<conditional name="params">
+		<param name="annotate_rfam" type="select" label="annotate rfam nocoding RNAs(excluding miRNA)">
+		  <option value="yes" selected="true">yes</option>
+		  <option value="no">no</option>
+		</param>
+		 <when value="yes">
+			<!--param name="rfam" type="data" label="rfam sequence file" /-->
+			<conditional name="reference_rfam">
+			  <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
+				<option value="indexed">Use a built-in index</option>
+				<option value="history">Use one from the history</option>
+			  </param>
+			  <when value="indexed">
+				<param name="index" type="select" label="Select a non-coding RNA reference" help="If your reference of interest is not listed, contact the Galaxy team">
+				  <options from_data_table="rfam_bowtie_indexes">
+					<filter type="sort_by" column="2"/>
+					<validator type="no_options" message="No indexes are available for the selected input dataset"/>
+				  </options>
+				</param>
+			  </when>
+			  <when value="history">
+				<param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference" />
+			  </when>
+			</conditional>
+
+			<param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches for rfam mapping"/>
+
+			<param name="delete_rfam" type="select" label="delet rfam mapped reads">
+			  <option value="yes" selected="true">yes</option>
+			  <option value="no">no</option>
+			</param>
+		 </when>
+
+    </conditional> 
+
+	<conditional name="mirbase">
+		<param name="known_microRNA" type="select" label="Analysis known microRNAs(eg. from mirbase)">
+		  <option value="yes" selected="true">yes</option>
+		  <option value="no">no</option>
+		 </param>
+		 <when value="yes">
+			<param name="mat" type="data" label="mature microRNA sequence file" />
+			<param name="pre" type="data" label="precursor microRNA sequence file" />
+		 </when>
+
+	</conditional>
+	
+
+	<param name="a" type="text" value="TGGAATTCTCGGGTGCCAAGG" label="3' adapter sequence" />
+	<param name="mapnt" type="integer" value="8" label="minimum adapter map nts" />
+	<param name="min" type="integer" value="19" label="minimum microRNA length" />
+	<param name="max" type="integer" value="28" label="maximum microRNA length" />
+	<param name="mismatch" type="integer" value="0" label="number of allowed mismatches when mapping reads to precursors" />
+	<param name="e" type="integer" value="2" label="number of nucleotides upstream of the mature sequence to consider" />
+	<param name="f" type="integer" value="5" label="number of nucleotides downstream of the mature sequence to consider" />
+	<param name="r" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" />
+	<param name="dis" type="integer" value="200" label="Maximal space between miRNA and miRNA*" />
+	<param name="flank" type="integer" value="10" label="Flank sequence length of miRNA precursor" />
+	<param name="mfe" type="float" value="-30" label="Maximal free energy allowed for a miRNA precursor" />
+  </inputs>
+
+  <outputs>
+   <data format="txt" name="known microRNA express list" from_work_dir="miRPlant_out/known_microRNA_express.txt" label="${tool.name} on ${on_string}: known microRNA express list">
+   <filter>(mirbase['known_microRNA'] == 'yes')</filter>
+   </data>
+   <data format="txt" name="known microRNA express alignment" from_work_dir="miRPlant_out/known_microRNA_express.aln" label="${tool.name} on ${on_string}: known microRNA express alignment">
+   <filter>(mirbase['known_microRNA'] == 'yes')</filter>
+   </data>
+   <data format="txt" name="known microRNA moRs result" from_work_dir="miRPlant_out/known_microRNA_express.moRs" label="${tool.name} on ${on_string}: known microRNA moRs result">
+   <filter>(mirbase['known_microRNA'] == 'yes')</filter>
+   </data>
+   <data format="txt" name="known microRNA precursor file" from_work_dir="miRPlant_out/known_microRNA_precursor.fa" label="${tool.name} on ${on_string}: known microRNA precursor file">
+   <filter>(mirbase['known_microRNA'] == 'yes')</filter>
+   </data>
+   <data format="txt" name="known microRNA mature file" from_work_dir="miRPlant_out/known_microRNA_mature.fa" label="${tool.name} on ${on_string}: known microRNA mature file">
+   <filter>(mirbase['known_microRNA'] == 'yes')</filter>
+   </data>
+   <data format="txt" name="novel microRNA express list" from_work_dir="miRPlant_out/novel_microRNA_express.txt" label="${tool.name} on ${on_string}: novel microRNA express list"/>
+   <data format="txt" name="novel microRNA precursor file" from_work_dir="miRPlant_out/novel_microRNA_precursor.fa" label="${tool.name} on ${on_string}: novel microRNA precursor file"/>
+   <data format="txt" name="novel microRNA mature sequence file" from_work_dir="miRPlant_out/novel_microRNA_mature.fa" label="${tool.name} on ${on_string}: novel microRNA mature sequence file"/>
+   <data format="html" name="analysis result" from_work_dir="miRPlant_out/result.html" label="${tool.name} on ${on_string}: analysis result"/>
+  </outputs>
+
+ <help>
+
+ </help>
+ </tool>