| Previous changeset 32:e70d58319eaa (2018-05-28) Next changeset 34:54cb93674556 (2018-06-17) |
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sRNAPipe.xml |
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| diff -r e70d58319eaa -r c1a5c5205b24 sRNAPipe.xml --- a/sRNAPipe.xml Mon May 28 12:27:23 2018 -0400 +++ b/sRNAPipe.xml Fri Jun 01 18:17:59 2018 -0400 |
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| b'@@ -1,236 +1,240 @@\n-<tool id="sRNAPipe" name="sRNAPipe" version="0.0.1">\r\n- <description>In-depth study of small RNA</description>\r\n- <command interpreter="perl">\r\n-\r\n- ./bin/sRNAPipe.pl\r\n-\r\n- --fastq ${first_input}\r\n- --fastq_n ${first_input.name}\r\n- #for $input_file in $input_files:\r\n- --fastq ${input_file.additional_input}\r\n- --fastq_n ${input_file.additional_input.name}\r\n- #end for\r\n-\r\n- #if $Genome.refGenomeSource == "history":\r\n- --ref "${Genome.ownFile}"\r\n- --build_index\r\n- #else:\r\n- --ref "${Genome.indices.fields.path}"\r\n- #end if\r\n-\r\n- #if $tRNAs.refGenomeSource == "history":\r\n- --tRNAs "${tRNAs.ownFile}"\r\n- --build_tRNAs\r\n- #elif $tRNAs.refGenomeSource == "none":\r\n- --tRNAs "None"\r\n- #else:\r\n- --tRNAs "${tRNAs.indices.fields.path}"\r\n- #end if\r\n-\r\n- #if $snRNAs.refGenomeSource == "history":\r\n- --snRNAs "${snRNAs.ownFile}"\r\n- --build_snRNAs\r\n- #elif $snRNAs.refGenomeSource == "none":\r\n- --snRNAs "None"\r\n- #else:\r\n- --snRNAs "${snRNAs.indices.fields.path}"\r\n- #end if\r\n-\r\n- #if $rRNAs.refGenomeSource == "history":\r\n- --rRNAs "${rRNAs.ownFile}"\r\n- --build_rRNAs\r\n- #elif $rRNAs.refGenomeSource == "none":\r\n- --rRNAs "None"\r\n- #else:\r\n- --rRNAs "${rRNAs.indices.fields.path}"\r\n- #end if\r\n-\r\n- #if $miRNAs.refGenomeSource == "history":\r\n- --miRNAs "${miRNAs.ownFile}"\r\n- --build_miRNAs\r\n- #else:\r\n- --miRNAs "${miRNAs.indices.fields.path}"\r\n- #end if\r\n-\r\n- #if $transcripts.refGenomeSource == "history":\r\n- --transcripts "${transcripts.ownFile}"\r\n- --build_transcripts\r\n- #else:\r\n- --transcripts "${transcripts.indices.fields.path}"\r\n- #end if\r\n-\r\n- #if $TE.refGenomeSource == "history":\r\n- --TE "${TE.ownFile}"\r\n- --build_TE\r\n- #else:\r\n- --TE "${TE.indices.fields.path}"\r\n- #end if\r\n-\r\n- --si_min $si_min\r\n- --si_max $si_max\r\n- --pi_min $pi_min\r\n- --pi_max $pi_max\r\n- --min $min\r\n- --max $max\r\n-\r\n- --mis $mis\r\n- --misTE $misTE\r\n- --dir $html_out.files_path\r\n- --html $html_out\r\n- --PPPon $PPPon\r\n- </command>\r\n-\r\n- <requirements>\r\n- <requirement type="package" version="0.7.12">bwa</requirement>\r\n- <requirement type="package" version="2.24">bedtools</requirement>\r\n- <requirement type="package" version="1.2">samtools</requirement>\r\n- </requirements>\r\n-\r\n- <inputs>\r\n- <param format="fastqsanger" name="first_input" type="data" label="fastqsanger (Q33)" help=""/>\r\n- <repeat name="input_files" title="Additional Fastq Files">\r\n- <param format="fastqsanger" name="additional_input" type="data" label="fastqsanger (Q33)" help=""/>\r\n- </repeat>\r\n- <conditional name="Genome">\r\n- <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">\r\n- <option value="indexed">Use a built-in index</option>\r\n- <option value="history">Use one from the history</option>\r\n- </param>\r\n- <when value="indexed">\r\n- <param name="indices" type="select" label="Select a reference genome">\r\n- <options from_data_table="bwa_indexes">\r\n- <filter type="sort_by" column="2" />\r\n- <validator type="no_options" message="No indexes are available" />\r\n- </options>\r\n- </param>\r\n- </when>\r\n- <when value="history">\r\n- <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />\r\n- </when>\r\n- </conditional>\r\n- <conditional name="transcripts">\r\n- <param name="refGenomeSource" type="select" label="Will you select transcripts database from your history or use a built-in index?">\r\n- <option value="indexed">Use a built-in index</option>\r\n- <option value="history">Use one from the history</option>\r\n- </param>\r\n- <when value="indexed">\r\n- <param name="indices" type="select" label="Select a transcripts refe'..b'om history" />\n+ </when>\n+ </conditional>\n+ <conditional name="snRNAs">\n+ <param name="refGenomeSource" type="select" label="Will you select snRNA database from your history or use a built-in index?">\n+ <option value="indexed">Use a built-in index</option>\n+ <option value="history">Use one from the history</option>\n+ <option value="none">None</option>\n+ </param>\n+ <when value="indexed">\n+ <param name="indices" type="select" label="Select a snRNAs reference">\n+ <options from_data_table="bwa_indexes">\n+ <filter type="sort_by" column="2" />\n+ <validator type="no_options" message="No indexes are available" />\n+ </options>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />\n+ </when>\n+ </conditional>\n+ <conditional name="rRNAs">\n+ <param name="refGenomeSource" type="select" label="Will you select rRNAs database from your history or use a built-in index?">\n+ <option value="indexed">Use a built-in index</option>\n+ <option value="history">Use one from the history</option>\n+ <option value="none">None</option>\n+ </param>\n+ <when value="indexed">\n+ <param name="indices" type="select" label="Select a rRNAs reference">\n+ <options from_data_table="bwa_indexes">\n+ <filter type="sort_by" column="2" />\n+ <validator type="no_options" message="No indexes are available" />\n+ </options>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />\n+ </when>\n+ </conditional>\n+ <conditional name="tRNAs">\n+ <param name="refGenomeSource" type="select" label="Will you select tRNA database from your history or use a built-in index?">\n+ <option value="indexed">Use a built-in index</option>\n+ <option value="history">Use one from the history</option>\n+ <option value="none">None</option>\n+ </param>\n+ <when value="indexed">\n+ <param name="indices" type="select" label="Select a tRNA reference">\n+ <options from_data_table="bwa_indexes">\n+ <filter type="sort_by" column="2" />\n+ <validator type="no_options" message="No indexes are available" />\n+ </options>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />\n+ </when>\n+ </conditional>\n+\n+ <param name="min" type="integer" value="18" label="minimum read size"/>\n+ <param name="max" type="integer" value="29" label="maximum read size"/>\n+ <param name="si_min" type="integer" value="21" label="lower bound of siRNA range"/> \n+ <param name="si_max" type="integer" value="21" label="higher bound of siRNA range"/>\n+ <param name="pi_min" type="integer" value="23" label="lower bound of piRNA range"/>\n+ <param name="pi_max" type="integer" value="29" label="higher bound of piRNA range"/>\n+\n+ <param name="mis" type="integer" value="0" label="maximal genome mismatches"/>\n+ <param name="misTE" type="integer" value="3" label="maximal TE mismatches"/>\n+ <param name="PPPon" type="boolean" checked="true" label="PPPartners"/>\n+ </inputs>\n+ <outputs>\n+ <data format="html" name="html_out" label="${tool.name}_${first_input.name}_${on_string}"/>\n+\n+ <collection format ="fastqsanger" type="list" label="${tool.name}_fastq_outputs" name="output_fastqsanger">\n+ <discover_datasets format ="fastqsanger" pattern="(?P<name>.*)" directory="fastq_dir" />\n+ </collection>\n+\n+ </outputs>\n+ <help>\n+ \t**User manual**\n+ \t"https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf"\n+ </help>\n+</tool>\n' |