Mercurial > repos > iuc > snpeff

diff snpEff_create_db.xml @ 30:0c8a8cd9dd5b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd
author iuc
date Sat, 28 Sep 2024 16:27:42 +0000
parents 030fe29d4c47
children b7029a54f73e
line wrap: on
line diff
--- a/snpEff_create_db.xml	Wed Aug 03 16:33:10 2022 +0000
+++ b/snpEff_create_db.xml	Sat Sep 28 16:27:42 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="snpEff_build_gb" name="SnpEff build:" version="@WRAPPER_VERSION@.galaxy5">
+<tool id="snpEff_build_gb" name="SnpEff build:" version="@WRAPPER_VERSION@.galaxy6" profile="22.01">
     <description> database from Genbank or GFF record</description>
     <macros>
         <import>snpEff_macros.xml</import>
@@ -14,25 +14,26 @@
             python3 '$__tool_directory__/gbk2fa.py' '${input_type.input}' '${output_fasta}' ${input_type.remove_version} &&
         #end if
 
-        mkdir -p '${snpeff_output.files_path}'/'${genome_version}' &&
+        mkdir -p '${snpeff_output.files_path}/${genome_version}' &&
+        mkdir -p snpeff_output/'${genome_version}' &&
 
         #if str($input_type.input_type_selector) == "gb":
             #if $input_type.input.is_of_type("genbank"):
-                ln -s '${input_type.input}' '${snpeff_output.files_path}/${genome_version}/genes.gbk' &&
+                ln -s '${input_type.input}' 'snpeff_output/${genome_version}/genes.gbk' &&
             #elif $input_type.input.is_of_type("genbank.gz"):
-                ln -s '${input_type.input}' '${snpeff_output.files_path}/${genome_version}/genes.gbk.gz' &&
+                ln -s '${input_type.input}' 'snpeff_output/${genome_version}/genes.gbk.gz' &&
             #end if
         #else:
             #if $input_type.reference_source.reference_source_selector == "history":
                 #if $input_type.reference_source.input_fasta.is_of_type("fasta"):
-                    ln -s '${input_type.reference_source.input_fasta}' '${snpeff_output.files_path}/${genome_version}/sequences.fa' &&
+                    ln -s '${input_type.reference_source.input_fasta}' 'snpeff_output/${genome_version}/sequences.fa' &&
                 #elif $input_type.reference_source.input_fasta.is_of_type("fasta.gz"):
-                    ln -s '${input_type.reference_source.input_fasta}' '${snpeff_output.files_path}/${genome_version}/sequences.fa.gz' &&
+                    ln -s '${input_type.reference_source.input_fasta}' 'snpeff_output/${genome_version}/sequences.fa.gz' &&
                 #end if
             #elif $input_type.reference_source.reference_source_selector == "cached":
-                ln -s '${input_type.reference_source.ref_file.fields.path}' '${snpeff_output.files_path}/${genome_version}/sequences.fa' &&
+                ln -s '${input_type.reference_source.ref_file.fields.path}' 'snpeff_output/${genome_version}/sequences.fa' &&
             #end if
-            ln -s '${input_type.input}' '${snpeff_output.files_path}/${genome_version}/genes.${input_type.input_type_selector}' &&
+            ln -s '${input_type.input}' 'snpeff_output/${genome_version}/genes.${input_type.input_type_selector}' &&
         #end if
 
         snpEff @JAVA_OPTIONS@ build -v
@@ -45,7 +46,8 @@
         #elif str($input_type.input_type_selector) == "gtf":
             -gtf22
         #end if
-        -dataDir '${snpeff_output.files_path}' '${genome_version}' &&
+        -dataDir "\$(pwd)/snpeff_output" '${genome_version}' &&
+        mv snpeff_output/'${genome_version}'/*.bin '${snpeff_output.files_path}/${genome_version}' &&
         echo '${genome_version}.genome : ${genome_version}' >> '${snpeff_output.files_path}'/snpEff.config &&
         echo '${genome_version}.codonTable : ${codon_table}' >> '${snpeff_output.files_path}'/snpEff.config
     ]]></command>
@@ -122,7 +124,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="genome_version" value="pBR322"/>
             <param name="input_type_selector" value="gb"/>
             <param name="input" value="pBR322.gbk" />
@@ -133,7 +135,7 @@
             </output>
             <output name="output_fasta" value="pBR322_test1.fna"/>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="genome_version" value="pBR322"/>
             <param name="input_type_selector" value="gb"/>
             <param name="input" value="pBR322.gbk.gz" />
@@ -144,7 +146,7 @@
             </output>
             <output name="output_fasta" value="pBR322_test1.fna"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="genome_version" value="pBR322"/>
             <param name="input_type_selector" value="gff"/>
             <param name="reference_source_selector" value="history"/>
@@ -156,7 +158,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="genome_version" value="pBR322"/>
             <param name="input_type_selector" value="gff"/>
             <param name="reference_source_selector" value="history"/>
@@ -168,7 +170,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="genome_version" value="Saccharomyces_mito"/>
             <param name="input_type_selector" value="gtf"/>
             <param name="reference_source_selector" value="history"/>