Galaxy |

Changeset 1:39edec572bae (2021-11-11)

Previous changeset 0:9d79beb19ac3 (2021-04-18) Next changeset 2:589078edd230 (2022-04-25)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 2612885d6ad86e41a08b0a2f29430d65f111ab66"

diff -r 9d79beb19ac3 -r 39edec572bae macros.xml
--- a/macros.xml Sun Apr 18 23:47:56 2021 +0000
+++ b/macros.xml Thu Nov 11 16:38:42 2021 +0000

@@ -1,12 +1,10 @@
<macros>
     <token name="@TOOL_VERSION@">1.3</token>
-    <xml name="edam_ontology">
-        <edam_topics>
-            <edam_topic>topic_0196</edam_topic>
-        </edam_topics>
-        <edam_operations>
-            <edam_operation>operation_0525</edam_operation>
-        </edam_operations>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">merqury</xref>
+        </xrefs>
     </xml>
     <xml name="requirements">
         <requirements>

diff -r 9d79beb19ac3 -r 39edec572bae merqury.xml
--- a/merqury.xml Sun Apr 18 23:47:56 2021 +0000
+++ b/merqury.xml Thu Nov 11 16:38:42 2021 +0000

[

b'@@ -1,9 +1,9 @@\n-<tool id="merqury" name="Merqury" version="@TOOL_VERSION@" profile="20.01">\n+<tool id="merqury" name="Merqury" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">\n <description>evaluate the assembly quality</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n- <expand macro="edam_ontology"/>\n+ <expand macro="bio_tools"/>\n <expand macro="requirements"/>\n <version_command>merqury --version</version_command>\n <command detect_errors="exit_code"><![CDATA[\n@@ -137,29 +137,44 @@\n </valid>\n </sanitizer>\n </param>\n+ <param name="output_selector" type="select" display="checkboxes" multiple="true" optional="true" label="Output options">\n+ <option value="qv" selected="true">QV stats</option>\n+ <option value="plots" selected="true">Plots</option>\n+ <option value="sizes">Size files</option>\n+ <option value="stats" selected="true">Stats file</option>\n+ <option value="bed">BED: hap-mer tracks</option>\n+ <option value="wig">WIG: hap-mer tracks</option>\n+ </param>\n </inputs>\n <outputs>\n- <collection name="bed_files" type="list" label="${tool.name} on ${on_string}: bed">\n+ <collection name="bed_files" type="list" label="${tool.name} on ${on_string}: BED files">\n <discover_datasets pattern="(?P<name>.+)\\.bed" format="bed" directory="output_files"/>\n+ <filter>"bed" in output_selector</filter>\n </collection>\n- <collection name="wig_files" type="list" label="${tool.name} on ${on_string}: wig">\n+ <collection name="wig_files" type="list" label="${tool.name} on ${on_string}: WIG files">\n <discover_datasets pattern="(?P<name>.+)\\.wig" format="wig" directory="output_files"/>\n+ <filter>"wig" in output_selector</filter>\n </collection>\n- <collection name="qv_files" type="list" label="${tool.name} on ${on_string}: qv">\n+ <collection name="qv_files" type="list" label="${tool.name} on ${on_string}: QV stats">\n <discover_datasets pattern="(?P<name>.+)\\.qv" format="tabular" directory="output_files"/>\n+ <filter>"qv" in output_selector</filter>\n </collection>\n- <collection name="png_files" type="list" label="${tool.name} on ${on_string}: png">\n+ <collection name="png_files" type="list" label="${tool.name} on ${on_string}: plots">\n <discover_datasets pattern="(?P<name>.+)\\.png" format="png" directory="output_files"/>\n+ <filter>"plots" in output_selector</filter>\n </collection>\n <collection name="sizes_files" type="list" label="${tool.name} on ${on_string}: size files">\n <discover_datasets pattern="(?P<name>.+)\\.sizes" format="tabular" directory="output_files"/>\n+ <filter>"sizes" in output_selector</filter>\n </collection>\n <collection name="stats_files" type="list" label="${tool.name} on ${on_string}: stats">\n <discover_datasets pattern="(?P<name>.+)\\.stats" format="tabular" directory="output_files"/>\n+ <filter>"stats" in output_selector</filter>\n </collection>\n </outputs>\n <tests>\n- <test>\n+ \n+ <test expect_num_outputs="2">\n <conditional name="mode">\n <param name="options" value="trio"/>\n <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/>\n@@ -171,42 +186,14 @@\n </conditional>\n </conditional>\n <param name="label" value="output_01"/>\n- <output_collection name="png_files" type="list" count="3">\n- <element name="output_01.assembly.mat.spectra-cn.ln" file="output_01.assembly.spectra-cn.ln.png" ftype="png">\n- <assert_contents>\n- <has_size value="2733" delta="100"/>'..b'nal>\n <param name="label" value="output_04"/>\n- <output_collection name="png_files" type="list" count="5">\n- <element name="output_04.assembly_01.mat.spectra-cn.ln" file="output_04.assembly_01.mat.spectra-cn.ln.png" ftype="png">\n- <assert_contents>\n- <has_size value="2733" delta="100"/>\n- </assert_contents>\n- </element>\n- <element name="output_04.assembly_01.pat.spectra-cn.ln" file="output_04.assembly_01.pat.spectra-cn.ln.png" ftype="png">\n- <assert_contents>\n- <has_size value="2733" delta="100"/>\n- </assert_contents>\n- </element>\n- <element name="output_04.assembly_02.mat.spectra-cn.ln" file="output_04.assembly_02.mat.spectra-cn.ln.png" ftype="png">\n- <assert_contents>\n- <has_size value="2733" delta="100"/>\n- </assert_contents>\n- </element>\n- <element name="output_04.assembly_02.pat.spectra-cn.ln" file="output_04.assembly_02.pat.spectra-cn.ln.png" ftype="png">\n- <assert_contents>\n- <has_size value="2733" delta="100"/>\n- </assert_contents>\n- </element>\n- <element name="output_04.hapmers.blob" file="output_04.hapmers.blob.png" ftype="png">\n- <assert_contents>\n- <has_size value="10764" delta="100"/>\n- </assert_contents>\n- </element>\n- </output_collection>\n- <output_collection name="stats_files" type="list" count="3">\n- <element name="output_04.assembly_01.100_20000.phased_block" ftype="tabular"/>\n- <element name="output_04.assembly_02.100_20000.phased_block" file="output_04.assembly_02.100_20000.phased_block.stats.tabular" ftype="tabular"/>\n- <element name="output_04.completeness"/>\n- </output_collection>\n+ <param name="output_selector" value="qv"/>\n <output_collection name="qv_files" type="list" count="1">\n <element name="output_04" file="output_04_qv.tabular" ftype="tabular"/>\n </output_collection>\n- <output_collection name="wig_files" type="list" count="4">\n- <element name="output_04.assembly_01.pat" ftype="wig"/>\n- <element name="output_04.assembly_01.mat" ftype="wig"/>\n- <element name="output_04.assembly_02.pat" ftype="wig"/>\n- <element name="output_04.assembly_02.mat" ftype="wig"/>\n- </output_collection>\n- <output_collection name="sizes_files" type="list" count="4">\n- <element name="output_04.assembly_01.100_20000.phased_block"/>\n- <element name="output_04.assembly_01.contig" file="output_04.assembly_01.contig.tabular" ftype="tabular"/>\n- <element name="output_04.assembly_02.100_20000.phased_block"/>\n- <element name="output_04.assembly_02.contig" file="output_04.assembly_02.contig.tabular" ftype="tabular"/>\n- </output_collection>\n- <output_collection name="bed_files" type="list" count="6">\n- <element name="output_04.assembly_01.100_20000.phased_block" ftype="bed"/>\n- <element name="output_04.assembly_01.100_20000.switch" file="output_04.assembly_01.100_20000.switch.bed" ftype="bed"/>\n- <element name="output_04.assembly_01.sort" file="output_04.assembly_01.sort.bed" ftype="bed"/>\n- <element name="output_04.assembly_02.100_20000.phased_block" ftype="bed"/>\n- <element name="output_04.assembly_02.100_20000.switch" ftype="bed"/>\n- <element name="output_04.assembly_02.sort" ftype="bed"/>\n- </output_collection>\n </test>\n </tests>\n <help><![CDATA[\n'

diff -r 9d79beb19ac3 -r 39edec572bae test-data/assembly.fasta.gz

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

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.assembly.100_20000.phased_block.blob.png

Binary file test-data/output_01.assembly.100_20000.phased_block.blob.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.assembly.bed
--- a/test-data/output_01.assembly.bed Sun Apr 18 23:47:56 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-tig00000005 227845 227853 pat
-tig00000005 426764 426772 pat

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.assembly.block.N.png

Binary file test-data/output_01.assembly.block.N.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.assembly.contig.tabular
--- a/test-data/output_01.assembly.contig.tabular Sun Apr 18 23:47:56 2021 +0000
+++ b/test-data/output_01.assembly.contig.tabular Thu Nov 11 16:38:42 2021 +0000

@@ -1,8 +1,2 @@
contig assembly 732575
-contig assembly 684532
-contig assembly 512140
-contig assembly 437616
-contig assembly 367569
-contig assembly 295265
-contig assembly 56868
-contig assembly 27107
+contig assembly 305392

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.assembly.continuity.N.png

Binary file test-data/output_01.assembly.continuity.N.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.assembly.mat.spectra-cn.ln.png

Binary file test-data/output_01.assembly.mat.spectra-cn.ln.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.assembly.pat.bed
--- a/test-data/output_01.assembly.pat.bed Sun Apr 18 23:47:56 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,3 +0,0 @@
-tig00000005 227825 227850 0.2
-tig00000005 227850 227875 0.12
-tig00000005 426750 426775 0.32

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.assembly.pat.spectra-cn.ln.png

Binary file test-data/output_01.assembly.pat.spectra-cn.ln.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.assembly.spectra-cn.ln.png

Binary file test-data/output_01.assembly.spectra-cn.ln.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.hapmers.blob.png

Binary file test-data/output_01.hapmers.blob.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_01.switches.txt
--- a/test-data/output_01.switches.txt Sun Apr 18 23:47:56 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-output_01.assembly.100_20000 switch error rate (%) (Num. switches / Total markers found): 0 2 0%

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_02.assembly.spectra-cn.fl.png

Binary file test-data/output_02.assembly.spectra-cn.fl.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_02.assembly.spectra-cn.ln.png

Binary file test-data/output_02.assembly.spectra-cn.ln.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_02.assembly.spectra-cn.st.png

Binary file test-data/output_02.assembly.spectra-cn.st.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_02.completeness.stats.tabular
--- a/test-data/output_02.completeness.stats.tabular Sun Apr 18 23:47:56 2021 +0000
+++ b/test-data/output_02.completeness.stats.tabular Thu Nov 11 16:38:42 2021 +0000

@@ -1,1 +1,1 @@
-assembly all 193949 279149 69.4787
+assembly all 32353 32353 100

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_02.spectra-asm.fl.png

Binary file test-data/output_02.spectra-asm.fl.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_02.spectra-asm.ln.png

Binary file test-data/output_02.spectra-asm.ln.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_02.spectra-asm.st.png

Binary file test-data/output_02.spectra-asm.st.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_02_qv.tabular
--- a/test-data/output_02_qv.tabular Sun Apr 18 23:47:56 2021 +0000
+++ b/test-data/output_02_qv.tabular Thu Nov 11 16:38:42 2021 +0000

@@ -1,1 +1,1 @@
-assembly 2882439 3113584
+assembly 0 1037953

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.assembly_01.spectra-cn.fl.png

Binary file test-data/output_03.assembly_01.spectra-cn.fl.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.assembly_01.spectra-cn.ln.png

Binary file test-data/output_03.assembly_01.spectra-cn.ln.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.assembly_01.spectra-cn.st.png

Binary file test-data/output_03.assembly_01.spectra-cn.st.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.assembly_02.spectra-cn.fl.png

Binary file test-data/output_03.assembly_02.spectra-cn.fl.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.assembly_02.spectra-cn.ln.png

Binary file test-data/output_03.assembly_02.spectra-cn.ln.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.assembly_02.spectra-cn.st.png

Binary file test-data/output_03.assembly_02.spectra-cn.st.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.completeness.stats.tabular
--- a/test-data/output_03.completeness.stats.tabular Sun Apr 18 23:47:56 2021 +0000
+++ b/test-data/output_03.completeness.stats.tabular Thu Nov 11 16:38:42 2021 +0000

@@ -1,3 +1,3 @@
-assembly_01 all 193949 279149 69.4787
-assembly_02 all 64441 279149 23.0848
-both all 193949 279149 69.4787
+assembly_01 all 32353 32353 100
+assembly_02 all 32353 32353 100
+both all 32353 32353 100

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.spectra-asm.ln.png

Binary file test-data/output_03.spectra-asm.ln.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.spectra-cn.fl.png

Binary file test-data/output_03.spectra-cn.fl.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.spectra-cn.ln.png

Binary file test-data/output_03.spectra-cn.ln.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03.spectra-cn.st.png

Binary file test-data/output_03.spectra-cn.st.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_03_qv.tabular
--- a/test-data/output_03_qv.tabular Sun Apr 18 23:47:56 2021 +0000
+++ b/test-data/output_03_qv.tabular Thu Nov 11 16:38:42 2021 +0000

@@ -1,3 +1,3 @@
-assembly_01 2882439 3113584
-assembly_02 964973 1037945
-Both 3847412 4151529
+assembly_01 0 1037953
+assembly_02 0 1037953
+Both 0 2075906

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_01.100_20000.phased_block.blob.png

Binary file test-data/output_04.assembly_01.100_20000.phased_block.blob.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_01.100_20000.switch.bed
--- a/test-data/output_04.assembly_01.100_20000.switch.bed Sun Apr 18 23:47:56 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-tig00000005 227845 227853 pat Same pat
-tig00000005 426764 426772 pat Same pat

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_01.bed
--- a/test-data/output_04.assembly_01.bed Sun Apr 18 23:47:56 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-tig00000005 227845 227853 pat
-tig00000005 426764 426772 pat

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_01.block.N.png

Binary file test-data/output_04.assembly_01.block.N.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_01.contig.tabular
--- a/test-data/output_04.assembly_01.contig.tabular Sun Apr 18 23:47:56 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,8 +0,0 @@
-contig assembly_01 732575
-contig assembly_01 684532
-contig assembly_01 512140
-contig assembly_01 437616
-contig assembly_01 367569
-contig assembly_01 295265
-contig assembly_01 56868
-contig assembly_01 27107

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_01.continuity.N.png

Binary file test-data/output_04.assembly_01.continuity.N.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_01.mat.spectra-cn.ln.png

Binary file test-data/output_04.assembly_01.mat.spectra-cn.ln.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_01.pat.bed
--- a/test-data/output_04.assembly_01.pat.bed Sun Apr 18 23:47:56 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,3 +0,0 @@
-tig00000005 227825 227850 0.2
-tig00000005 227850 227875 0.12
-tig00000005 426750 426775 0.32

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_01.pat.spectra-cn.ln.png

Binary file test-data/output_04.assembly_01.pat.spectra-cn.ln.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_01.sort.bed
--- a/test-data/output_04.assembly_01.sort.bed Sun Apr 18 23:47:56 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-tig00000005 227845 227853 pat
-tig00000005 426764 426772 pat

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_02.contig.tabular
--- a/test-data/output_04.assembly_02.contig.tabular Sun Apr 18 23:47:56 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-contig assembly_02 732575
-contig assembly_02 305392

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_02.mat.spectra-cn.ln.png

Binary file test-data/output_04.assembly_02.mat.spectra-cn.ln.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.assembly_02.pat.spectra-cn.ln.png

Binary file test-data/output_04.assembly_02.pat.spectra-cn.ln.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.hapmers.blob.png

Binary file test-data/output_04.hapmers.blob.png has changed

diff -r 9d79beb19ac3 -r 39edec572bae test-data/output_04.switches.txt
--- a/test-data/output_04.switches.txt Sun Apr 18 23:47:56 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,1 +0,0 @@
-output_04.assembly_02.100_20000 switch error rate (%) (Num. switches / Total markers found):

diff -r 9d79beb19ac3 -r 39edec572bae test-data/read-db.meryldb

Binary file test-data/read-db.meryldb has changed