# HG changeset patch
# User tyty
# Date 1419013127 18000
# Node ID 245551867ad14bfc58d89d168e9fce8011a9f096
# Parent  8b25759cc83a6d7c793858a6ba3e5180b1831743
Deleted selected files

diff -r 8b25759cc83a -r 245551867ad1 Iterative_mapping/iterative_map.xml
--- 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>
diff -r 8b25759cc83a -r 245551867ad1 get_reads/get_read.xml
--- 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>
diff -r 8b25759cc83a -r 245551867ad1 predict/predict_RNAs.xml
--- 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>
diff -r 8b25759cc83a -r 245551867ad1 reactivity_cal/reactivity_calculation.xml
--- 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>