Mercurial > repos > big-tiandm > mirplant2

diff miRPlant.xml @ 50:7b5a48b972e9 draft

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Uploaded
author big-tiandm
date Fri, 05 Dec 2014 00:11:02 -0500
parents f008ab2cadc6
children 8b8c356e6db5
line wrap: on
line diff
--- a/miRPlant.xml	Wed Dec 03 02:03:27 2014 -0500
+++ b/miRPlant.xml	Fri Dec 05 00:11:02 2014 -0500
@@ -15,10 +15,6 @@
   <command interpreter="perl">miRPlant.pl 
    ## Change this to accommodate the number of threads you have available.
         -t \${GALAXY_SLOTS:-4}
-   ## Do or not delet rfam mapped tags
-    #if $params.delet_rfam == "yes":
-	-D 
-	#end if
 	-path \$SCRIPT_PATH
 
     #for $j, $s in enumerate( $series )
@@ -27,7 +23,43 @@
     -tag ${s.tag}
     #end for
 
-    -format $format -gfa $gfa -pre $pre -mat $mat -rfam $rfam  -a $a -M $mapnt -min $min -max $max -mis $mismatch -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe > run.log
+      ## prepare bowtie index
+      #set index_path = ''
+      #if str($reference_genome.source) == "history":
+          bowtie-build "$reference_genome.own_file" genome; ln -s "$reference_genome.own_file" genome.fa;
+          #set index_path = 'genome'
+      #else:
+          #set index_path = $reference_genome.index.fields.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.annotate_rfam.reference_rfam.source) == "history":
+			  bowtie-build "$params.annotate_rfam.reference_rfam.own_file" rfam; ln -s "$params.annotate_rfam.reference_rfam.own_file" rfam.fa;
+			  #set rfam_index_path = 'rfam'
+		  #else:
+			  #set rfam_index_path = $params.annotate_rfam.reference_rfam.index.fields.path
+		  #end if
+
+		-rfam ${rfam_index_path}.fa -idx2 $rfam_index_path -v $v 
+	   ## Do or not delet rfam mapped tags
+		#if $params.annotate_rfam.rfamresult.delet_rfam == "yes":
+		-D 
+		#end if
+	#end if
+
+
+   ## Do or not annotate known microRNAs
+    #if $params.known_microRNA == "yes":
+	-pre $pre -mat $mat 
+	#end if
+
+
+    -format $format -gfa ${index_path}.fa -idx $index_path -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>
@@ -37,25 +69,136 @@
      <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/>
    </repeat>
 
+        <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="delet_rfam" type="select" label="delet rfam mapped reads">
+		<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 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"/>
+
+			<conditional name="rfamresult">
+				<param name="delet_rfam" type="select" label="delet rfam mapped reads">
+				  <option value="yes" selected="true">yes</option>
+				  <option value="no">no</option>
+				 </param>
+			</conditional> <!-- params -->
+		 
+		 
+		 </when>
     </conditional> <!-- params -->
 
+
 	<!--param name="input" format="tabular"  type="data" label="input config file" /-->
 	
 	<param name="format" type="select" lable="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="gfa"  type="data" label="genome sequence fasta file"/>
+
+	<param name="phred" type="select" lable="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>
+
 	<!--param type="data" name="index" label="genome sequence bowtie index"/-->
-	<param name="mat" type="data" label="mature microRNA sequence file" />
-	<param name="pre" type="data" label="precursor microRNA sequence fie" />
-	<param name="rfam" type="data" label="rfam sequence file" />
+	<conditional name="params">
+		<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 fie" />
+		 </when>
+    </conditional> <!-- params -->
+
+	<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" /-->
+		 <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 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"/>
+		 </when>
+    </conditional> <!-- params -->
+
 	<!--param type="data" name="idx2" label="rfam sequence bowtie index " -->
 	<param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" />
 	<param name="mapnt" type="integer" value="8" label="minimum adapter map nts" />
@@ -64,7 +207,6 @@
 	<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="v" type="integer" value="0" label="report end-to-end hits less than v mismatches"/>
 	<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" />
@@ -72,11 +214,21 @@
   </inputs>
 
   <outputs>
-   <data format="txt" name="known microRNA express list" from_work_dir="miRPlant_out/known_microRNA_express.txt" label="${tool.name} on ${on_string}: known microRNA express list"/>
-   <data format="txt" name="known microRNA express alignment" from_work_dir="miRPlant_out/known_microRNA_express.aln" label="${tool.name} on ${on_string}: known microRNA express alignment"/>
-   <data format="txt" name="known microRNA moRs result" from_work_dir="miRPlant_out/known_microRNA_express.moRs" label="${tool.name} on ${on_string}: known microRNA moRs result"/>
-   <data format="txt" name="known microRNA precursor file" from_work_dir="miRPlant_out/known_microRNA_precursor.fa" label="${tool.name} on ${on_string}: known microRNA precursor file"/>
-   <data format="txt" name="known microRNA mature file" from_work_dir="miRPlant_out/known_microRNA_mature.fa" label="${tool.name} on ${on_string}: known microRNA mature file"/>
+   <data format="txt" name="known microRNA express list" from_work_dir="miRPlant_out/known_microRNA_express.txt" label="${tool.name} on ${on_string}: known microRNA express list">
+   <filter>(params['known_microRNA'] == 'Yes')</filter>
+   </data>
+   <data format="txt" name="known microRNA express alignment" from_work_dir="miRPlant_out/known_microRNA_express.aln" label="${tool.name} on ${on_string}: known microRNA express alignment">
+   <filter>(params['known_microRNA'] == 'Yes')</filter>
+   </data>
+   <data format="txt" name="known microRNA moRs result" from_work_dir="miRPlant_out/known_microRNA_express.moRs" label="${tool.name} on ${on_string}: known microRNA moRs result">
+   <filter>(params['known_microRNA'] == 'Yes')</filter>
+   </data>
+   <data format="txt" name="known microRNA precursor file" from_work_dir="miRPlant_out/known_microRNA_precursor.fa" label="${tool.name} on ${on_string}: known microRNA precursor file">
+   <filter>(params['known_microRNA'] == 'Yes')</filter>
+   </data>
+   <data format="txt" name="known microRNA mature file" from_work_dir="miRPlant_out/known_microRNA_mature.fa" label="${tool.name} on ${on_string}: known microRNA mature file">
+   <filter>(params['known_microRNA'] == 'Yes')</filter>
+   </data>
    <data format="txt" name="novel microRNA express list" from_work_dir="miRPlant_out/novel_microRNA_express.txt" label="${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"/>