Mercurial > repos > big-tiandm > mirplant2
diff miRPlant.xml @ 50:7b5a48b972e9 draft
Uploaded
author | big-tiandm |
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date | Fri, 05 Dec 2014 00:11:02 -0500 |
parents | f008ab2cadc6 |
children | 8b8c356e6db5 |
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--- 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"/>