Mercurial > repos > tyty > structurefold
changeset 83:245551867ad1 draft
Deleted selected files
| author | tyty |
|---|---|
| date | Fri, 19 Dec 2014 13:18:47 -0500 |
| parents | 8b25759cc83a |
| children | c3092769835e |
| files | Iterative_mapping/iterative_map.xml get_reads/get_read.xml predict/predict_RNAs.xml reactivity_cal/reactivity_calculation.xml |
| diffstat | 4 files changed, 0 insertions(+), 285 deletions(-) [+] |
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--- a/Iterative_mapping/iterative_map.xml Fri Dec 12 16:39:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,96 +0,0 @@ -<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>
--- a/get_reads/get_read.xml Fri Dec 12 16:39:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ -<tool id="get_read_pipeline" name="Get RT Stop Counts" version="1.0"> - <description></description> - <command interpreter="python">get_read.py $lib_file $map_file $output </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> - </requirements> - <inputs> - <param name="lib_file" type="data" format="fasta" label="Reference genome/transcriptome"/> - <param name="map_file" type="data" format="bam" label="Mapped file"/> - </inputs> - <outputs> - <data name="output" format="txt"/> - </outputs> - <tests> - <test> - <param name="lib_file" value="test.bam" /> - <param name="map_file" value="com_rna.txt" /> - <output name="output" file="get_RT_stop_test.out" /> - </test> - </tests> - <help> - - -**TIPS**: - ------ - -**Input** - -* 1. A mapped (bam) file from Bowtie (or any other mapping program) -* 2. Reference library sequences (fasta) used to map the reads to - ------ - -**Output**: - -A text file with reverse transcription stop counts mapped to each nucleotide (RTSC file) - - - - </help> -</tool>
--- a/predict/predict_RNAs.xml Fri Dec 12 16:39:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,85 +0,0 @@ -<tool id="predict_pipeline" name="RNA Structure Prediction" version="1.0"> - <description></description> - <command interpreter="python"> - #if $reactivity.type == "restraint" - predict_RNAs.py $rna_list $reference_file $reactivity.type $temperature $output $reactivity.reactivity_file $reactivity.slope $reactivity.intercept - #else - predict_RNAs.py $rna_list $reference_file $reactivity.type $temperature $output - #end if - </command> - <stdio> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> - <requirements> - <requirement type="package" version="1.61">biopython</requirement> - <requirement type="package" version="1.7.1">numpy</requirement> - <requirement type="package" version="1.2.1">matplotlib</requirement> - </requirements> - <inputs> - <param name="rna_list" type="data" format="txt" label="List of RNA ids to predict"/> - <param name="reference_file" type="data" format="fasta" label="Reference genome/transcriptome"/> - <param name="temperature" type="float" value="310.15" label="Temperature (K)"/> - <conditional name="reactivity"> - <param name="type" type="select" label="RNA structure prediction type"> - <option value="silico">In silico</option> - <option value="restraint">With experimental restraints</option> - </param> - <when value="silico"/> - <when value="restraint"> - <param name="reactivity_file" type="data" label="Reactivity file"/> - <param name="slope" type="float" value="1.8" label="Slope used with structural restraints"/> - <param name="intercept" type="float" value="-0.6" label="Intercept used with structural restraints"/> - </when> - </conditional> - - </inputs> - <outputs> - <data name="output" format=".tar"/> - </outputs> - - <help> - - -**TIPS**: - ------ - -**Input**: - -* 1. A file with transcript Ids (Max num. 100), (each ID one line) -* 2. Reference file (fasta) used to map the reads to -* 3. Temperature for RNA structure prediction -* [Optional]: -* 1. A reactivity file with structural reactivity for each nucleotide on the sequence provided -* 2. Slope used with structural restraints (default 1.8) -* 3. Intercept used with structural restraints (default -0.6) - ------ - -**Output**: - -* 1. .ct files with predicted RNA structures [transciptID.ct] -* 2. .ps files which depict the predicted RNA structures [[transciptID.ps] -* [Optional] -* 3. .png files that shows the distribution of the reactivity of each nucleotide on the transcripts of interest. [transciptID.png] - ------ - -**Attention** - -Make sure any of the transcript Ids does not contain "|" or space! - ------ - -**Backend program**: - -* 1. This module is using RNAstructure (http://rna.urmc.rochester.edu/RNAstructure.html) as the backend program to predict RNA structures. -* 2. Default parameters are used for RNAstructure expect -T (Temperature), -sm (slope used with SHAPE restraints) and -si (intercept used with SHAPE restraints) which users can specify the value - - - - </help> -</tool>
--- a/reactivity_cal/reactivity_calculation.xml Fri Dec 12 16:39:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,60 +0,0 @@ -<tool id="react_cal_pipeline" name="Reactivity Calculation" version="1.0"> - <description></description> - <command interpreter="python">react_cal.py $dist_file1 $dist_file2 $seq_file $nt_spec $flag_in $threshold $output </command> - <requirements> - <requirement type="package" version="1.61">biopython</requirement> - <requirement type="package" version="1.7.1">numpy</requirement> - </requirements> - <inputs> - <param name="dist_file1" type="data" format="txt" label="RTSC file for (+) library"/> - <param name="dist_file2" type="data" format="txt" label="RTSC file for (-) library"/> - <param name="seq_file" type="data" format="fasta" label="Reference genome/transcriptome"/> - <param name="nt_spec" type="select" label="Nucleotide specificity"> - <option value="AC">AC</option> - <option value="ATCG">AUCG</option> - </param> - <param name="flag_in" type="boolean" checked="true" truevalue = "1" falsevalue = "0" label="Normalization is performed if checked"/> - <param name="threshold" type="float" value = "7" optional = "true" label="Threshold to cap the reactivities"/> - </inputs> - <outputs> - <data name="output" format="txt"/> - </outputs> - <tests> - <test> - <param name="dist_file1" value="dis_f_N1Ap_rrna.txt" /> - <param name="dist_file2" value="dis_f_N1Am_rrna.txt" /> - <param name="seq_file" value="rRNA.txt" /> - <param name="nt_spec" value="AC" /> - <param name="flag_in" value="1" /> - <param name="threshold" value="7" /> - <output name="output" file="DMS_reactivities.out" /> - - </test> - </tests> - - <help> - - -**TIPS**: - ------ - -**Input**: - -* 1. RTSC files (Output of Get RT Stop Counts) for (+) and (-) library -* 2. Reference file (fasta) used to map the reads to -* 3. Nucleotide Specificity (Type of nucleotides to have reactivity, e.g. AC for DMS and ACTG for SHAPE) -* [Optional]: -* 1. A threshold to cap the structural reactivities. {Default: 7} -* 2. Flag that determines whether to perform 2%-8% normalization {Default: Yes} - ------ - -**Output**: - -A text file with structural reactivity for each nucleotide (Reactivity file) - - - - </help> -</tool>