diff epic2/epic2_wrapper.xml @ 2:601ad3ea888b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/epic2/epic2_wrapper.xml	Wed May 08 08:11:56 2019 -0400
@@ -0,0 +1,372 @@
+<tool id="epic2" name="epic2" version="@VERSION@.0">
+    <description>peak calling of broad ChIP-Seq marks</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+   <expand macro="requirements" />
+    
+    <stdio>
+        <exit_code range="1:125" level="fatal" description="Unknown error occurred" />
+        <exit_code range="130:" level="fatal" description="Unknown error occurred" />
+        <regex match="epic2: (command ){0,1}not found" source="stderr" level="fatal" description="The epic2 python package is not properly installed, contact Galaxy administrators" />
+    </stdio>
+    
+    <command><![CDATA[
+
+        ##set up treatment files, extension must be bed, bedpe, bam, sam
+        #set $t_file_list = list()
+        #if str($treatment.t_multi_select) == "No":
+            #if $treatment.input_treatment_file.is_of_type('bed')
+                #set $t_file = 'ChIP_file.bed'
+                ln -s '$treatment.input_treatment_file' $t_file &&
+            #elif $treatment.input_treatment_file.is_of_type('bam')
+                #set $t_file = 'ChIP_file.bam'
+                ln -s '$treatment.input_treatment_file' $t_file &&
+                ln -s '$treatment.input_treatment_file.metadata.bam_index' ${t_file}.bai &&
+            #elif $treatment.input_treatment_file.is_of_type('sam')
+                #set $t_file = 'ChIP_file.sam'
+                ln -s '$treatment.input_treatment_file' $t_file &&
+            #end if
+            $t_file_list.append($t_file)
+        #else
+            #set $inputs = $treatment.input_treatment_file
+            #for $i, $f in enumerate($inputs)
+                #if $f.is_of_type('bed')
+                    #set $t_file = ''.join(['ChIP_file_',str($i),'.bed'])
+                    ln -s '$f' $t_file &&
+                #elif $f.is_of_type('bam')
+                    #set $t_file = ''.join(['ChIP_file_',str($i),'.bam'])
+                    ln -s '$f' $t_file &&
+                    ln -s '$f.metadata.bam_index' ${t_file}.bai &&
+                #elif $f.is_of_type('sam')
+                    #set $t_file = ''.join(['ChIP_file_',str($i),'.sam'])
+                    ln -s '$f' $t_file &&
+                #end if
+                $t_file_list.append($t_file)
+            #end for
+        #end if
+
+        ##set up control files, extension must be bed, bedpe, bam, sam
+        #if str($control.c_select) == "Yes":
+            #set $c_file_list = list()
+            #if str($control.c_multiple.c_multi_select) == "No":
+                #set $f = $control.c_multiple.input_control_file
+                #if $f.is_of_type('bed')
+                    #set $c_file = 'control_file.bed'
+                    ln -s '$f' $c_file &&
+                #elif $f.is_of_type('bam')
+                    #set $c_file = 'control_file.bam'
+                    ln -s '$f' $c_file &&
+                    ln -s '$f.metadata.bam_index' ${c_file}.bai &&
+                #elif $f.is_of_type('sam')
+                    #set $c_file = 'control_file.sam'
+                    ln -s '$f' $c_file &&
+                #end if
+                $c_file_list.append($c_file)
+            #else
+                #set $inputs = $control.c_multiple.input_control_file
+                #for $i, $f in enumerate($inputs)
+                    #if $f.is_of_type('bed')
+                        #set $c_file = ''.join(['control_file',str($i),'.bed'])
+                        ln -s '$f' $c_file &&
+                    #elif $f.is_of_type('bam')
+                        #set $c_file = ''.join(['control_file',str($i),'.bam'])
+                        ln -s '$f' $c_file &&
+                        ln -s '$f.metadata.bam_index' ${c_file}.bai &&
+                    #elif $f.is_of_type('sam')
+                        #set $c_file = ''.join(['control_file',str($i),'.sam'])
+                        ln -s '$f' $c_file &&
+                    #end if
+                    $c_file_list.append($c_file)
+                #end for
+            #end if
+        #end if
+
+        epic2
+
+            ## Treatment File(s)
+            -t ${ ' '.join( $t_file_list ) }
+
+            ## Control File(s)
+            #if str($control.c_select) == "Yes":
+                -c ${ ' '.join( $c_file_list ) }
+            #end if
+
+            ## Predefined or Custom Genome
+            #if str($genome.g_select) == "Yes":
+                --genome ${genome.builtin_genome}
+            #else
+                #if str($genome.chromsizes.chr_select) == "No":
+                    #if $genome.chromsizes.cs_file.is_of_type('fasta'):
+                        --chromsizes <(awk '/^>/ {if (seqlen) print seqlen;printf substr($1,2) "\t";seqlen=0;next}
+                            {seqlen+=length($0)}END{print seqlen}' '${genome.chromsizes.cs_file}')
+                    #else
+                        --chromsizes ${genome.chromsizes.cs_file}
+                    #end if
+                #else
+                    #if $genome.chromsizes.builtin_fasta.fields.path
+                        --chromsizes <(awk '/^>/ {if (seqlen) print seqlen;printf substr($1,2) "\t";seqlen=0;next}
+                            {seqlen+=length($0)}END{print seqlen}' '${genome.chromsizes.builtin_fasta.fields.path}')
+                    #end if
+                #end if
+            #end if
+            #if $genome.egf:
+                --effective-genome-fraction ${genome.egf}
+            #end if
+
+            #if $fdr:
+                -fdr $fdr
+            #end if
+
+        ## BAM OPTIONS
+        #if $bam_options.required_flag:
+            --required-flag $bam_options.required_flag
+        #end if
+
+        #if $bam_options.filter_flag:
+            --filter-flag $bam_options.filter_flag
+        #end if
+
+        #if $bam_options.mapq:
+            --mapq $bam_options.mapq
+        #end if
+
+        #if $bam_options.autodetect_chroms:
+            --autodetect-chroms
+        #end if
+
+        #if $bam_options.discard_chroms:
+            --discard-chromosomes-pattern $bam_options.discard_chroms
+        #end if
+
+        ## ADVANCED OPTIONS
+        #if $advanced_options.keep_dupes:
+            --keep-duplicates
+        #end if
+
+        #if $advanced_options.bin_size:
+            --bin-size $advanced_options.bin_size
+        #end if
+
+        #if $advanced_options.gaps_allowed:
+            --gaps-allowed $advanced_options.gaps_allowed
+        #end if
+
+        #if $advanced_options.fragment_size:
+            --fragment-size $advanced_options.fragment_size
+        #end if
+
+        #if $advanced_options.original_algorithm:
+            --original-algorithm
+        #end if
+
+        > ${peaks} 
+        2> >(awk 'NF' >&2)
+
+        #if $to_bed:
+            && 
+            awk 'NR>1{if ($4==0) {pv=50;qv=50}else{pv=-log($4)/log(10);qv=-log($9)/log(10)};
+            print $1,$2,$3,"island_"NR-1,int($5),$6,$10,pv,qv}' OFS="\t" ${peaks} > ${bed_peaks}
+        #end if
+
+    ]]></command>
+    
+    <inputs>
+        <conditional name="treatment">
+            <param name="t_multi_select" type="select" label="Are you pooling Treatment Files?" help="" >
+                <option value="No" selected="True">No</option>
+                <option value="Yes">Yes</option>
+            </param>
+            <when value="No" >
+                <param name="input_treatment_file" argument="-t" type="data" format="bam,sam,bed" label="ChIP-Seq Treatment File" help="(-t)" />
+            </when>
+            <when value="Yes">
+                <param name="input_treatment_file" argument="-t" type="data" format="bam,sam,bed" multiple="true" 
+                       label="ChIP-Seq Treatment File" help="(-t)" />
+            </when>
+        </conditional>
+
+        <conditional name="control">
+            <param name="c_select" type="select" label="Do you have a Control File?" >
+                <option value="Yes">Yes</option>
+                <option value="No" selected="True">No</option>
+            </param>
+            <when value="Yes">
+                <conditional name="c_multiple">
+                    <param name="c_multi_select" type="select" label="Are you pooling Control Files?" help="" >
+                        <option value="No" selected="True">No</option>
+                        <option value="Yes">Yes</option>
+                    </param>
+                    <when value="No" >
+                        <param name="input_control_file" argument="-c" type="data" format="bam,sam,bed" label="ChIP-Seq Control File" help="(-c)" />
+                    </when>
+                    <when value="Yes">
+                        <param name="input_control_file" argument="-c" type="data" format="bam,sam,bed" multiple="true" 
+                               label="ChIP-Seq Control File" help="(-c)" />
+                    </when>
+                </conditional>
+            </when>
+            <when value="No">
+                <param name="evalue" argument="-e" type="integer" optional="True" label="e-value" 
+                       help="The E-value controls the genome-wide error rate of identified islands under the random 
+                             background assumption. Should be used when not using a control library. Default 1000." />
+            </when>
+        </conditional>
+
+        <conditional name="genome">
+            <param name="g_select" type="select" label="Is your genome indexed?" >
+                <option value="Yes" selected="True">Yes</option>
+                <option value="No">No</option>
+            </param>
+            <when value="Yes">
+                <expand macro="effectiveGenomeSize" />
+                <param name="egf" argument="-egf" type="float" min="0" max="1" optional="True" label="Effective genome fraction" 
+                       help="Use a different effective genome fraction than the one included in epic2, which depends on genome and readlength. (-egf)" />
+            </when>
+            <when value="No">
+                <conditional name="chromsizes">
+                    <param name="chr_select" type="select" label="Do you want to use an indexed fasta file?" 
+                           help="Chromosome sizes will be calculated from the provided fasta file." >
+                        <option value="No">No</option>
+                        <option value="Yes" selected="True">Yes</option>
+                    </param>
+                    <when value="No" >
+                        <param name="cs_file" argument="--chromsizes" type="data" format="fasta,txt,tabular,tsv" label="Chromosome sizes" 
+                               help="Provide a fasta file for automated calculation, or a tab-separated file with 
+                                     two columns: chromosome names and sizes. (--chromsizes)" />
+                    </when>
+                    <when value="Yes">
+                        <param name="builtin_fasta" argument="--chromsizes" type="select" optional="True" label="Genome for fasta file" help="(--chromsizes)" >
+                            <options from_data_table="fasta_indexes">
+                                <filter type="sort_by" column="2" />
+                                <validator type="no_options" message="No indexes are available" />
+                            </options>
+                        </param>
+                    </when>
+                </conditional>
+                <param name="egf" argument="-egf" type="float" min="0" max="1" optional="True" label="Effective genome fraction" 
+                       help="The effective genome fraction is the proportion of the genome that is mappable, excluding Ns. (-egf)" />
+            </when>
+        </conditional>
+
+            <param name="fdr" argument="-fdr" type="float" min="0" max="1" optional="True" label="False discovery rate cutoff" 
+                   help="Remove all islands with an FDR above cutoff. Default 0.05 (-fdr)" />
+
+            <param name="to_bed" type="boolean" checked="false" label="Print output in bed format?"/>
+
+        <section name="bam_options" title="BAM Options">
+            <param name="required_flag" argument="--required-flag" type="integer" optional="True" label="Required flag" 
+                   help="Keep reads with these bits set in flag. Same as `samtools view -f`. Default 0. (--required-flag)" />
+            <param name="filter_flag" argument="--filter-flag" type="integer" optional="True" label="Filter flag" 
+                   help="Discard reads with these bits set in flag. Same as `samtools view -F`. Default 1540 (hex: 0x604). (--filter-flag)" />
+            <param name="mapq" argument="--mapq" type="integer" optional="True" label="Mapping quality" 
+                   help="Discard reads with mapping quality lower than this. Default 5. (--mapq)" />
+            <param name="autodetect_chroms" type="boolean" checked="false" truevalue="--autodetect-chroms" falsevalue="" label="Autodetect chromosomes?" 
+                   help="Autodetect chromosomes from bam file. Use with --discard-chromosomes flag to avoid non-canonical chromosomes. (--autodetect-chroms)" />
+            <param name="discard_chroms" argument="--discard-chromosomes-pattern" type="text" optional="True" label="Discard chromosomes pattern" 
+                   help="Discard reads from chromosomes matching
+                        this pattern. Default '_'. Note that if you are not
+                        interested in the results from non-canonical
+                        chromosomes, you should ensure they are removed with
+                        this flag, otherwise they will make the statistical
+                        analysis too stringent. (--discard-chromosomes-pattern)"/>
+        </section>
+        
+        <section name="advanced_options" title="Advanced Options">
+            <param name="keep_dupes" type="boolean" checked="false" truevalue="--keep-duplicates" falsevalue="" label="Keep duplicates?" 
+                   help="Keep reads mapping to the same position on the same strand within a library. (--keep-duplicates)" />
+            <param name="bin_size" argument="--bin-size" type="integer" optional="True" label="Bin size" 
+                   help="Size of the windows to scan the genome. BIN-SIZE is the smallest possible island. Default 200. (--bin-size)" />
+            <param name="gaps_allowed" argument="--gaps-allowed" type="integer" optional="True" label="Gaps allowed" 
+                   help="This number is multiplied by the window size to determine the number of gaps (ineligible windows) allowed 
+                         between two eligible windows. Default 3. (--gaps-allowed)"/>
+            <param name="fragment_size" argument="--fragment-size" type="integer" optional="True" label="Fragment size" 
+                   help="(Single end reads only) Size of the sequenced fragment. Each read is extended half the fragment size from the 5' end. 
+                         Default 150 (i.e. extend by 75). (--fragment-size)" />
+            <param name="original_algorithm" type="boolean" checked="false" truevalue="--original-algorithm" falsevalue="" 
+                   label="Compute p-values with SICER original algorithm?" 
+                   help="Use the original SICER algorithm, without the epic2 fix. This will use all reads in your files to compute
+                        the p-values, including those falling outside the genome boundaries. (--original-algorithm)" />
+        </section>
+   </inputs>
+
+    <outputs>
+        <data format="tabular" name="peaks" label="${tool.name} on ${on_string}"/>
+        <data format='bed' name='bed_peaks' label="${tool.name} on ${on_string}: BED">
+            <filter>to_bed</filter>
+        </data>
+
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_treatment_file" value="test.bam" ftype="bam" />
+            <param name="c_select" value="Yes" />
+            <param name="input_control_file" value="control.bam" ftype="bam"/>
+            <output name="peaks" file="epic2_results.txt"/>
+        </test>
+        <test>
+            <param name="input_treatment_file" value="test.bed.gz" ftype="bed" />
+            <param name="c_select" value="Yes" />
+            <param name="input_control_file" value="control.bed.gz" ftype="bed"/>
+            <output name="peaks" file="epic2_results1.txt"/>
+        </test>
+        <test>
+            <param name="input_treatment_file" value="test_ChIP.bam" ftype="bam" />
+            <param name="c_select" value="Yes" />
+            <param name="input_control_file" value="test_Input.bam" ftype="bam"/>
+            <param name="g_select" value="No" />
+            <param name="chr_select" value="No" />
+            <param name="cs_file" value="test_chromsizes.txt" />
+            <param name="egf" value="0.99" />
+            <param name="original_algorithm" value="Yes" />
+            <output name="peaks" file="epic2_results2.txt"/>
+        </test>
+        <test>
+            <param name="input_treatment_file" value="test_ChIP.bam" ftype="bam" />
+            <param name="c_select" value="Yes" />
+            <param name="input_control_file" value="test_Input.bam" ftype="bam"/>
+            <param name="g_select" value="No" />
+            <param name="chr_select" value="No" />
+            <param name="cs_file" value="test_fasta.fasta" />
+            <param name="egf" value="0.99" />
+            <param name="to_bed" value="Yes" />
+            <param name="mapq" value="10" />
+            <param name="bin_size" value="100" />
+            <param name="gaps_allowed" value="0" />
+            <output name="peaks" file="epic2_results3.txt"/>
+            <output name="bed_peaks" file="epic2_results3.bed"/>
+        </test>
+    </tests>
+
+    <help>
+Chip-Seq broad peak/domain finder based on SICER.
+
+**Accepted input formats**
+
+Input file extension must be bed, bedpe, bam or sam.
+
+**Broad peaks format**
+        
+Original epic2 output does not follow any standard format, then broad peaks bed format is offered. This format follows the standard from ENCODE, BED 6 + 3, and contains the following columns:
+        
+        * **1.** Chrom 
+        * **2.** Start 
+        * **3.** End 
+        * **4.** Name 
+        * **5.** Score 
+        * **6.** Strand 
+        * **7.** log2FoldChange 
+        * **8.** -log10PValue 
+        * **9.** -log10FDR
+        
+.. class:: warningmark
+
+        On columns 8 and 9, the max value is set to 50 when Pvalue == 0.0.
+
+Tool adapted to Galaxy by Miriam Payá Milans. Original documentation on https://github.com/biocore-ntnu/epic2.
+        
+        
+    </help>
+    <expand macro="citations" />
+</tool>