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Changeset 1:c7fda6e88567 (2024-10-01)

Previous changeset 0:ca2743037241 (2022-09-27) Next changeset 2:c97f8a687258 (2024-10-02)

Commit message:
planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty

modified:
kmc.xml
kmc_tools_filter.xml
kmc_tools_simple.xml
kmc_tools_transform.xml
macros.xml

added:
test-data/Illumina.1.fastq.gz
test-data/Illumina.2.fastq.gz
test-data/kmer_27.kmc_pre
test-data/kmer_27.kmc_suf
test-data/statistic_27.json_bk
test-data/test.fasta.gz

removed:
test-data/db.kmc_pre
test-data/db.kmc_suf

diff -r ca2743037241 -r c7fda6e88567 kmc.xml
--- a/kmc.xml Tue Sep 27 05:20:06 2022 +0000
+++ b/kmc.xml Tue Oct 01 04:06:26 2024 +0000

[

b'@@ -1,91 +1,233 @@\n-<tool id="kmc" name="KMC Counter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >\n+<tool id="kmc" name="KMC Counter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n <description>K-mer counting and filtering of reads</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n <xrefs>\n <xref type=\'bio.tools\'>kmc</xref>\n </xrefs> \n- <macros>\n-\t <import>macros.xml</import>\n- </macros>\n <expand macro="requirements" />\n <expand macro="stdio" />\n <expand macro="version_command" /> \n <command><![CDATA[\n-\t kmc\n+ mkdir output &&\n+\t #if $data_type.select == \'individual\'\n+\t #for $input_file in $data_type.individual_file\n+\t #if $input_file.is_of_type("fastq","fastq.gz","fastqsanger.gz"):\n+ #if $input_file.ext.endswith(".gz")\n+ #set $ext=\'.fastq.gz\'\n+ #else\n+ #set $ext=\'.fastq\'\n+ #end if\n+ ln -s \'$input_file\' \'in$ext\' &&\n+ #elif $input_file.is_of_type("fasta","fasta.gz"):\n+ #if $input_file.ext.endswith(".gz")\n+ #set $ext=\'.fasta.gz\'\n+ #else\n+ #set $ext=\'.fasta\'\n+ #end if\n+ ln -s \'$input_file\' \'in$ext\' &&\n+ #elif $input_file.is_of_type("bam"):\n+ ln -s \'$input_file\' in.bam &&\n+ #elif $input_file.is_of_type("kmc_suf"):\n+ #if $input_file.ext.endswith(".kmc_suf")\n+ #set $suf_ext=\'.kmc_suf\'\n+ #end if\n+ #if $input_file.ext.endswith(".kmc_pre")\n+ #set $pre_ext=\'.kmc_pre\'\n+ #end if\n+ ln -s \'$input_file\' \'in$suf_ext\' &&\n+ ln -s \'$input_file\' \'in$pre_ext\' &&\n+\t #end if\n+\t #end for\n+\t #else \n+\t \tmkdir input_dir &&\n+\t\t#import re\n+\t \t#for $input_file in $data_type.collection_file\n+\t\t #if $input_file.is_of_type("fastq","fastq.gz","fastqsanger.gz"):\n+ #if $input_file.ext.endswith(".gz")\n+ #set $ext=\'.fastq.gz\'\n+ #else\n+ #set $ext=\'.fastq\'\n+ #end if\n+ \t #set $identifier = re.sub(\'[^\\s\\w\\-\\\\.]\', \'_\', str($input_file.element_identifier))\n+\t \t ln -s \'$input_file\' \'input_dir/${identifier}\' &&\n+\t\t #elif $input_file.is_of_type("fasta","fasta.gz"):\n+\t \t #if $input_file.ext.endswith(".gz")\n+\t \t \t#set $ext=\'.fasta.gz\'\n+\t \t #else\n+\t \t\t#set $ext=\'.fasta\'\n+\t \t #end if\n+\t \t #set $identifier = re.sub(\'[^\\s\\w\\-\\\\.]\', \'_\', str($input_file.element_identifier))\n+\t \t ln -s \'$input_file\' \'input_dir/${identifier}\' &&\n+\t \t #elif $input_file.is_of_type("bam"):\n+\t \t #set $identifier = re.sub(\'[^\\s\\w\\-\\\\.]\', \'_\', str($input_file.element_identifier))\n+\t \t ln -s \'$input_file\' \'input_dir/${identifier}\' &&\n+\t\t #elif $input_file.is_of_type("kmc_suf"):\n+\t \t #if $input_file.ext.endswith(".kmc_suf")\n+\t \t\t#set $suf_ext=\'.kmc_suf\'\n+\t \t #end if\n+\t \t #if $input_file.ext.endswith(".kmc_pre")\n+\t \t\t#set $pre_ext=\'.kmc_pre\'\n+\t \t #end if\n+\t \t #set $identifier = re.sub(\'[^\\s\\w\\-\\\\.]\', \'_\', str($input_file.element_identifier))\n+\t \t ln -s \'$input_file\' \'input_dir/${identifier}\' &&\n+\t \t ln -s \'$input_file\' \'input_dir/${identifier}\' &&\n+\t\t #end if\n+\t \t#end for\n+\t \tls -ld input_dir/* | awk \'{print $9}\' >> files.list &&\n+\t #end if\n+\n+\t kmc\n \t -t\\${GALAXY_SLOTS:-4}\n \t #if $params.k:\n \t \t-k\'$params.k\'\t\t\n \t #end if\n-\t #if $params.m:\n-\t -m\'$params.m\'\n-\t #end if\n+\t -m\\${GALAXY_MEMORY_GB:-4}\n \t #if $params.j:\n \t -j\'$statistic\'\n \t #end if\n-\t #if $params.exclude_length:\n-\t -ci\'$params.exclude_length\'\n+\t #if $params.p:\n+\t -p\'$params.p\'\n+\t #end if\n+\t #if $params.ci:\n+\t -ci\'$params.ci\'\n+\t '..b'le" value="test.fasta.gz" ftype="fasta.gz"/>\n+ <param name="k" value="27" />\n+ <param name="ci" value="2" />\n+ <param name="cs" value="255" />\n+ <output_collection name="kmc_db" type="list">\n+ <element name="kmer_27.kmc_pre" file="kmer_27.kmc_pre" ftype="binary" />\n+ <element name="kmer_27.kmc_suf" file="kmer_27.kmc_suf" ftype="binary" />\n+ </output_collection>\n+ <output name="statistic" ftype="json">\n+ <assert_contents>\n+ <has_text text="1st_stage"/>\n+ <has_text text="2nd_stage"/>\n+ <has_text text="Stats"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+\t  \n+\t \n+ \n+\t \n- <param name="input_file" value="contigs.fa" ftype="fasta"/> \n- <param name="k" value="27" />\n- <param name="m" value="24" />\n+\t <param name="cs" value="255" />\n+\t <output_collection name="kmc_db" type="list">\n+\t \t<element name="kmer_25.kmc_pre" file="kmer_25.kmc_pre" ftype="binary" />\n+\t \t<element name="kmer_25.kmc_suf" file="kmer_25.kmc_suf" ftype="binary" />\n+\t </output_collection>\n+\t <output name="statistic" ftype="json">\n+\t\t <assert_contents>\n+ <has_text text="1st_stage"/>\n+ <has_text text="2nd_stage"/>\n+ <has_text text="Stats"/>\n+\t\t </assert_contents>\t\t\t\t \n+\t </output>\n+ \t</test> -->\n+\t\n+ \n+ \n+ \n </tests>\n <help><![CDATA[\n \t \n'

diff -r ca2743037241 -r c7fda6e88567 kmc_tools_filter.xml
--- a/kmc_tools_filter.xml Tue Sep 27 05:20:06 2022 +0000
+++ b/kmc_tools_filter.xml Tue Oct 01 04:06:26 2024 +0000

@@ -1,4 +1,4 @@
-<tool id="kmc_filter" name="KMC filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
+<tool id="kmc_filter" name="KMC filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>filtering KMC's database</description>
     <xrefs>
         <xref type='bio.tools'>kmc</xref>

diff -r ca2743037241 -r c7fda6e88567 kmc_tools_simple.xml
--- a/kmc_tools_simple.xml Tue Sep 27 05:20:06 2022 +0000
+++ b/kmc_tools_simple.xml Tue Oct 01 04:06:26 2024 +0000

@@ -1,4 +1,4 @@
-<tool id="kmc_simple" name="KMC simple" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
+<tool id="kmc_simple" name="KMC simple" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>simple operations for two input kmer sets</description>
     <xrefs>
         <xref type='bio.tools'>kmc</xref>

diff -r ca2743037241 -r c7fda6e88567 kmc_tools_transform.xml
--- a/kmc_tools_transform.xml Tue Sep 27 05:20:06 2022 +0000
+++ b/kmc_tools_transform.xml Tue Oct 01 04:06:26 2024 +0000

@@ -1,4 +1,4 @@
-<tool id="kmc_transform" name="KMC transform" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
+<tool id="kmc_transform" name="KMC transform" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>single KMC's database</description>
     <xrefs>
         <xref type='bio.tools'>kmc</xref>

diff -r ca2743037241 -r c7fda6e88567 macros.xml
--- a/macros.xml Tue Sep 27 05:20:06 2022 +0000
+++ b/macros.xml Tue Oct 01 04:06:26 2024 +0000

[

@@ -1,6 +1,7 @@
<macros>
     <token name="@TOOL_VERSION@">3.2.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@PROFILE@">22.05</token>
     <xml name="requirements">
   <requirements>
<requirement type="package" version="@TOOL_VERSION@">kmc</requirement>
@@ -18,7 +19,18 @@
       ]]></version_command>
   </xml>
   <xml name="macro_input">
-       <param name="input_file" type="data" format="fasta,fastq,fasta.gz,fastqsanger,fastq.gz,bam" label="Sequence file"/>
+     <conditional name="data_type">
+            <param name="select" type="select" label="File input type for KMC">
+ <option value="individual">In individual datasets</option>
+ <option value="collection">In collection</option>
+     </param>
+            <when value="individual">
+ <param name="individual_file" type="data" format="fasta,fastq,fasta.gz,fastqsanger,fastqsanger.gz,fastq.gz,bam" multiple="true" label="FASTQ/A file"/>
+            </when>
+            <when value="collection">
+ <param name="collection_file" type="data_collection" collection_type="list" format="fasta,fastq,fasta.gz,fastqsanger,fastqsanger.gz,fastq.gz,bam" label="A list of FASTQ/A files"/>
+            </when>
+      </conditional>
   </xml>
   <xml name="general_option">
        <param argument="exclude_length" type="integer" value="2" label="exclude k-mers occurring less than [value] times (default: 2)"/>

diff -r ca2743037241 -r c7fda6e88567 test-data/Illumina.1.fastq.gz

Binary file test-data/Illumina.1.fastq.gz has changed

diff -r ca2743037241 -r c7fda6e88567 test-data/Illumina.2.fastq.gz

Binary file test-data/Illumina.2.fastq.gz has changed

diff -r ca2743037241 -r c7fda6e88567 test-data/db.kmc_pre

Binary file test-data/db.kmc_pre has changed

diff -r ca2743037241 -r c7fda6e88567 test-data/db.kmc_suf

Binary file test-data/db.kmc_suf has changed

diff -r ca2743037241 -r c7fda6e88567 test-data/kmer_27.kmc_pre

Binary file test-data/kmer_27.kmc_pre has changed

diff -r ca2743037241 -r c7fda6e88567 test-data/kmer_27.kmc_suf

Binary file test-data/kmer_27.kmc_suf has changed

diff -r ca2743037241 -r c7fda6e88567 test-data/statistic_27.json_bk
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/statistic_27.json_bk Tue Oct 01 04:06:26 2024 +0000

@@ -0,0 +1,15 @@
+{
+ "1st_stage": "0.077217s",
+ "2nd_stage": "1.20559s",
+ "Total": "1.28281s",
+ "Tmp_size": "0MB",
+ "Stats": {
+ "#k-mers_below_min_threshold": 124352,
+ "#k-mers_above_max_threshold": 0,
+ "#Unique_k-mers": 186071,
+ "#Unique_counted_k-mers": 61719,
+ "#Total no. of k-mers": 283537,
+ "#Total_reads": 2,
+ "#Total_super-k-mers": 26721
+ }
+}

diff -r ca2743037241 -r c7fda6e88567 test-data/test.fasta.gz

Binary file test-data/test.fasta.gz has changed