diff nanopolish_eventalign.xml @ 0:bee42f615f28 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nanopolish_eventalign.xml	Wed May 30 11:55:18 2018 -0400
@@ -0,0 +1,128 @@
+<tool id="nanopolish_eventalign" name="Nanopolish eventalign" version="0.1.0">
+    <description>- Align nanopore events to reference k-mers</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$input_merged' reads.fasta && 
+        
+        #if $input_reads_raw.extension == 'fast5':
+            mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 &&
+        #else
+            ln -s '$input_reads_raw' fast5_files.tar.gz &&
+            mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files &&
+        #end if
+
+        nanopolish index -d fast5_files/ reads.fasta &&
+        ln -s '$b' reads.bam &&
+        ln -s '${b.metadata.bam_index}' reads.bam.bai &&
+        ln -s '$g' genome.fa &&
+        
+        nanopolish eventalign
+        -r reads.fasta
+        -b reads.bam
+        -g genome.fa
+        $samples
+        $scale_events
+        $sam
+        $print_read_names
+        #if $w and str($w).strip():
+          -w "${w}"
+        #end if        
+        #if $input_models_fofn:
+          --models-fofn '$input_models_fofn'
+        #end if
+        #if $summary:
+            --summary eventalign-summary.txt
+        #end if
+        > eventalign.out
+
+
+    ]]></command>
+    <inputs>
+      <!-- index inputs -->
+        <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
+        <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz" label="Flat archive file of raw fast5 files"/>
+
+        <!-- variants consensus inputs -->
+        <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
+        <param type="data" argument="-g" format="fasta" label="The reference genome"/>
+
+        <!-- optional inputs -->
+        <param type="data" name="input_models_fofn" argument="--models-fofn" format="txt" optional="true"
+            label="Read alternative k-mer models (optional)" />
+        
+        <!-- optional params -->
+        <param argument="-w" type="text" optional="true"
+            label="find variants in window of region chromsome:start-end" />
+
+        <!-- optional flags -->
+        <param argument="--summary" type="boolean" truevalue="--summary" falsevalue="" checked="true"
+            label="Summarize the alignment of each read/strand" />
+        <param argument="--samples" type="boolean" truevalue="--samples" falsevalue="" checked="false"
+            label="Write the raw samples for the event to the tsv output" />
+        <param name="scale_events" argument="--scale-events" type="boolean" truevalue="--scale-events" falsevalue="" checked="false"
+            label="Scale events to the model, rather than vice-versa" />
+        <param argument="--sam" type="boolean" truevalue="--sam" falsevalue="" checked="false"
+            label="write output in SAM format" />
+        <param name="print_read_names" argument="--print-read-names" type="boolean" truevalue="--print-read-names" falsevalue="" checked="false"
+            label="Print read names instead of indexes" />
+
+    </inputs>
+
+    <outputs>
+      <!-- variants consensus outputs -->
+        <data name="output_summary" format="txt" from_work_dir="eventalign-summary.txt" label="eventalign summary of reads/strands" />
+        <data name="output_eventalign" format="txt" from_work_dir="eventalign.out" label="Computed variants"/>
+    </outputs>
+    <tests>
+        <test>
+      <!-- index test -->
+            <param name="input_merged" ftype="fasta" value="reads.fasta" />
+            <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
+            
+      <!-- variants consensus test -->
+            <param name="b" value="reads.sorted.bam" />
+            <param name="g" value="draft.fa" />
+            <param name="w" value="tig00000001:200000-200010" />
+            <param name="sam" value="true" />
+
+            <output name="output_summary" file="eventalign-summary.txt" />
+            <output name="output_eventalign" file="reads-draft.eventalign.sam"/>
+        </test>
+        <test>
+      <!-- index test -->
+            <param name="input_merged" ftype="fasta" value="reads.fasta" />
+            <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
+            
+      <!-- variants consensus test -->
+            <param name="b" value="reads.sorted.bam" />
+            <param name="g" value="draft.fa" />
+            <param name="w" value="tig00000001:200000-200010" />
+            <param name="sam" value="false" />
+            <param name="summary" value="false" />
+            <param name="scale_events" value="true" />
+            <param name="print_read_names" value="true" />
+
+            <output name="output_summary" file="t2-eventalign-summary.txt" />
+            <output name="output_eventalign"> 
+                <assert_contents>
+                    <has_text text="contig" />
+                    <has_text text="position" />
+                    <has_text text="event_index" />
+                    <has_text text="tig00000001" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Usage: nanopolish eventalign [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa
+        Align nanopore events to reference k-mers
+
+        Tutorial and manual available at:
+        http://nanopolish.readthedocs.io/en/latest/quickstart_eventalign.html      
+        
+        ]]></help>
+    <expand macro="citations" />
+</tool>