Mercurial > repos > bgruening > nanopolish_variants

changeset 8:bec636361cfd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
author bgruening
date Thu, 30 Nov 2023 17:57:59 +0000
parents a3afc5f0a96c
children
files macros.xml nanopolish_variants.xml
diffstat 2 files changed, 58 insertions(+), 43 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Fri Jul 30 06:29:50 2021 +0000
+++ b/macros.xml	Thu Nov 30 17:57:59 2023 +0000
@@ -1,5 +1,8 @@
 <macros>
-    <token name="@VERSION@">0.13.2</token>
+    <token name="@VERSION@">0.14.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">22.01</token>
+
     <xml name="requirements">
         <requirements>
         <requirement type="package" version="@VERSION@">nanopolish</requirement>
@@ -19,6 +22,52 @@
             <output name="output_index_readdb" file="reads.fasta.index.readdb" />
  -->
 
+
+    <token name="@PREPROCESS_INPUTS@"><![CDATA[
+        ln -s '$input_merged' reads.fasta && 
+ 
+        mkdir fast5_files &&
+        #if $input_reads_raw.extension == 'fast5':
+             ln -s '$input_reads_raw' fast5_files/read1.fast5 &&
+
+        #else if $input_reads_raw.extension == 'fast5.tar':
+            ln -s '$input_reads_raw' fast5_files.tar &&
+            tar -xf fast5_files.tar -C fast5_files &&
+
+        #else if $input_reads_raw.extension == 'fast5.tar.bz2':
+            ln -s '$input_reads_raw' fast5_files.tar.bz2 &&
+            tar -xjf fast5_files.tar.bz2 -C fast5_files &&
+
+        #else if $input_reads_raw.extension == 'fast5.tar.xz':
+            ln -s '$input_reads_raw' fast5_files.tar.xz &&
+            tar -xf fast5_files.tar.xz -C fast5_files &&
+
+        #else if $input_reads_raw.extension == 'fast5.tar.gz':
+            ln -s '$input_reads_raw' fast5_files.tar.gz &&
+            tar -xzf fast5_files.tar.gz -C fast5_files &&
+
+        #else:
+            echo 'Unsupported fast5 input type' &&
+            exit 1 &&
+
+        #end if
+
+        nanopolish index 
+        -d fast5_files/
+        #if $adv.input_seq_summary:
+          -s '$adv.input_seq_summary'
+        #end if 
+        reads.fasta &&
+
+        ln -s '$b' reads.bam &&
+        ln -s '${b.metadata.bam_index}' reads.bam.bai &&
+        #if $reference_source.reference_source_selector == 'history':
+            ln -f -s '$reference_source.ref_file' genome.fa &&
+        #else:
+            ln -f -s '$reference_source.ref_file.fields.path' genome.fa &&
+        #end if
+    ]]></token>
+
     <xml name="citations">
         <citations>
             <citation type="doi">10.1038/nmeth.3444</citation>
--- a/nanopolish_variants.xml	Fri Jul 30 06:29:50 2021 +0000
+++ b/nanopolish_variants.xml	Thu Nov 30 17:57:59 2023 +0000
@@ -1,43 +1,11 @@
-<tool id="nanopolish_variants" name="Nanopolish variants" version="@VERSION@+galaxy0">
+<tool id="nanopolish_variants" name="Nanopolish variants" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>- Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        ln -s '$input_merged' reads.fasta && 
-        
-        #if $input_reads_raw.extension == 'fast5':
-            mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 &&
-
-        #else if $input_reads_raw.extension == 'fast5.tar':
-            ln -s '$input_reads_raw' fast5_files.tar &&
-            mkdir fast5_files && tar -xf fast5_files.tar -C fast5_files &&
-
-        #else if $input_reads_raw.extension == 'fast5.tar.bz2':
-            ln -s '$input_reads_raw' fast5_files.tar.bz2 &&
-            mkdir fast5_files && tar -xjf fast5_files.tar.bz2 -C fast5_files &&
-
-        #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/
-        #if $adv.input_seq_summary:
-          -s '$adv.input_seq_summary'
-        #end if 
-        reads.fasta &&
-        
-        ln -s '$b' reads.bam &&
-        ln -s '${b.metadata.bam_index}' reads.bam.bai &&
-        #if $reference_source.reference_source_selector == 'history':
-            ln -f -s '$reference_source.ref_file' genome.fa &&
-        #else:
-            ln -f -s '$reference_source.ref_file.fields.path' genome.fa &&
-        #end if
+        @PREPROCESS_INPUTS@
         
         nanopolish variants
         -r reads.fasta
@@ -89,11 +57,11 @@
           --models-fofn '$input_models_fofn'
         #end if
 
-        && 
-
-        nanopolish vcf2fasta --skip-checks -g genome.fa variants.vcf > polished.fa
-
-
+        &&
+        nanopolish vcf2fasta
+            --skip-checks
+            -g genome.fa
+            variants.vcf > polished.fa
     ]]></command>
     <inputs>
       <!-- index inputs -->
@@ -131,7 +99,6 @@
        </section>
 
         <!-- optional params -->
-        <!-- optional params -->
         <param argument="-w" type="text" optional="true"
             label="find variants in window of region chromsome:start-end" />
         <param name="methylation_aware" type="text" optional="true" label="methylation aware polishing and test motifs given" help="(-q)"/>
@@ -251,8 +218,7 @@
     <help><![CDATA[
 
         Build an index mapping from basecalled reads to the signals measured by the sequencer
-        and
-        Find SNPs using a signal-level HMM
+        and find SNPs using a signal-level HMM.
 
         Tutorial and manual available at:
         http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html