diff chira_extract.xml @ 0:0a3107204741 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chira_extract.xml	Sun Jan 19 16:31:03 2020 -0500
@@ -0,0 +1,130 @@
+<tool id="chira_extract" name="ChiRA extract" version="@WRAPPER_VERSION@0">
+    <description>extrat the chimeras</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="aggressive"><![CDATA[
+        #set $genomic_fasta = ''
+        #if str($annotation.annot_choice) == "yes":
+            #if str($annotation.fasta_source.fasta_source_selector) == 'history':
+                #set $genomic_fasta = '$annotation.fasta_source.fasta'
+            #else
+                #set $genomic_fasta = '$annotation.fasta_source.fasta_id.fields.path'
+            #end if
+        #end if
+        chira_extract.py
+        -l '$loci'
+        #if str($annotation.annot_choice) == "yes":
+            -g '$annotation.gtf'
+            #if $hybridize:
+                -f '$genomic_fasta'
+            #end if
+        #end if
+        -tc '$tpm_cutoff'
+        -sc '$score_cutoff'
+        -co '$chimeric_overlap'
+        #if str($reference.ref_type) == "single":
+            -f1 '$ref_fasta'
+        #else if str($reference.ref_type) == "split":
+            -f1 '$ref_fasta1'
+            -f2 '$ref_fasta2'
+        #end if        
+        '$hybridize'
+        -p "\${GALAXY_SLOTS:-2}"
+        -o ./
+    ]]></command>
+
+    <inputs>
+        <param format="tabular" name="loci" type="data" label="File containing CRLs information"/>
+        <conditional name="annotation">
+            <param name="annot_choice" type="select" label="Have genomic information?"
+                   help="Selecet Yes if you have an annotation file and provide corresponding genomic fasta file">
+                <option value="yes">Yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="yes">
+                <param format="gtf,gff" name="gtf" type="data" label="Annotations in GTF format"/>
+                <conditional name="fasta_source">
+                    <param name="fasta_source_selector" type="select" label="Choose the source for the FASTA file">
+                        <option value="history" selected="true">History</option>
+                        <option value="preloaded">Server indexed files</option>
+                    </param>
+                    <when value="history">
+                        <param name="fasta" type="data" format="fasta" label="FASTA file" />
+                    </when>
+                    <when value="preloaded">
+                       <param name="fasta_id" type="select">
+                          <options from_data_table="fasta_indexes" />
+                       </param>
+                    </when>
+                </conditional>
+            </when>
+            <when value="no">
+                <!-- Do nothing -->
+            </when>        
+        </conditional>
+        <param name="tpm_cutoff" type="float" value="0" label="TPM cut-off" min="0" max="1"
+               help="Transcripts with less than this percentile TPMs will be discarded in the final output. [0-1.0]"/>
+        <param name="score_cutoff" type="float" value="0" label="Score cut-off" min="0" max="2"
+               help="Hybrids with less than this score will be discarded in the final output. [0-2.0]"/>
+        <param name="chimeric_overlap" type="integer" value="2"
+               label=" Maximum number of bases allowed between the chimericsegments of a read"/>
+        <conditional name="reference">
+            <param name="ref_type" type="select" label="Did you use single or split reference for alignment?">
+                <option value="split">Split reference</option>
+                <option value="single">Single reference</option>
+            </param>
+            <when value="split">
+                <param format="fasta" name="ref_fasta1" type="data" label="Reference FASTA file"
+                       help="Reference fasta file"/>
+                <param format="fasta" name="ref_fasta2" type="data" label="Second reference FASTA file"
+                       help="Second reference fasta file."/>
+            </when>
+            <when value="single">
+                <param format="fasta" name="ref_fasta" type="data" label="Reference FASTA file"
+                       help="Reference fasta file"/>
+            </when>
+        </conditional>
+        <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false" />
+    </inputs>
+    
+    <outputs>
+        <data format="tabular" name="chimeras" from_work_dir="chimeras" label="ChiRA chimeric reads on ${on_string}"/>
+        <data format="tabular" name="singletons" from_work_dir="singletons" label="ChiRA singleton reads on ${on_string}"/>
+    </outputs>
+    
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="loci" value="loci.counts"/>
+            <param name="ref_type" value="split"/>
+            <param name="ref_fasta1" value="ref1.fasta"/>
+            <param name="ref_fasta2" value="ref2.fasta"/>
+            <param name="annot_choice" value="no"/>
+            <param name="hybridize" value="true" />
+            <output name="chimeras" file="chimeras" sort="True"/>
+            <output name="singletons" file="singletons" sort="True"/>
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**What it does**
+
+This tool extracts the best chimeric alignments for each read. User can optionally hybridize the loci where the chimeric arms are mapping to. 
+
+**Inputs**
+
+  * Tabular file containing CRLs information
+  * Annotation GTF file
+  * Reference fasta files. Provide both in case of split reference.
+  * If your alignments are merged at genomic level in previous step (chira merge), then provide a reference genomic fasta fille.
+
+**Output**
+
+  * Tabular file containing chimeras information
+    </help>
+    <expand macro="citations" />
+</tool>
+