changeset 13:c4bde687c846 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 0cfd88d16b0b20a66d4b21b037ddee6a8c440d88
author iuc
date Wed, 12 Apr 2023 15:09:05 +0000
parents 290a11559985
children
files circos.xml macros.xml macros_tests.xml process-cytogenetic-bands.py stack-histogram.py stack-histogram.xml tableviewer.xml test-data/2/out.tar test-data/3/chrom.tab test-data/3/out.png test-data/too-many.fa
diffstat 11 files changed, 696 insertions(+), 58 deletions(-) [+]
line wrap: on
line diff
--- a/circos.xml	Mon Nov 22 12:23:12 2021 +0000
+++ b/circos.xml	Wed Apr 12 15:09:05 2023 +0000
@@ -1,11 +1,6 @@
 <?xml version="1.0"?>
-<tool id="circos" name="Circos" version="@WRAPPER_VERSION@">
+<tool id="circos" name="Circos" version="@WRAPPER_VERSION@" profile="21.09">
     <description>visualizes data in a circular layout</description>
-    <xrefs>
-        <xref type="bio.tools">galactic_circos</xref>
-        <!--<xref type="bioconda">circos</xref>-->
-        <!--<xref type="rrid">RRID:SCR_018207</xref>-->
-    </xrefs>
     <macros>
         <import>macros.xml</import>
         <import>macros_conffiles.xml</import>
@@ -18,6 +13,11 @@
     <edam_operations>
         <edam_operation>operation_0337</edam_operation>
     </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">galactic_circos</xref>
+        <!--<xref type="bioconda">circos</xref>-->
+        <!--<xref type="rrid">RRID:SCR_018207</xref>-->
+    </xrefs>
     <expand macro="requirements"/>
     <stdio>
       <!-- Anything other than zero is an error -->
@@ -29,10 +29,10 @@
     <version_command>circos --version</version_command>
     <command><![CDATA[
 ## Directory structure
-mkdir -p circos/conf/ circos/data/ &&
+mkdir -p circos/conf/ circos/data/;
 
 #if $reference_genome.ref.ref_source == 'history':
-    ln -s '$reference_genome.ref.genome_fasta' genomeref.fa &&
+    ln -s '$reference_genome.ref.genome_fasta' genomeref.fa;
 #end if
 
 #if $reference_genome.ref.ref_source in ('lengths', 'cached'):
@@ -48,61 +48,61 @@
                 <(head -n 50 '${reference_genome.ref.fasta_indexes.fields.len_path}')
             #end if
         #end if
-        > circos/conf/karyotype.txt &&
+        > circos/conf/karyotype.txt;
 #else if $reference_genome.ref.ref_source == 'karyotype':
-    cp $reference_genome.ref.input_karyotype circos/conf/karyotype.txt &&
+    cp '${reference_genome.ref.input_karyotype}' circos/conf/karyotype.txt;
 #else if str($reference_genome.ref.ref_source) == 'history':
     ## Process the karyotype.txt file
     python
         '$__tool_directory__/karyotype-from-fasta.py'
         genomeref.fa
-        > circos/conf/karyotype.txt &&
+        > circos/conf/karyotype.txt;
 #else if $reference_genome.ref.ref_source == 'preset':
-    cp '$__tool_directory__/karyotype/${reference_genome.ref.preset_karyotype}' circos/conf/karyotype.txt &&
+    cp '$__tool_directory__/karyotype/${reference_genome.ref.preset_karyotype}' circos/conf/karyotype.txt;
 #end if
 
 python '$__tool_directory__/karyotype-colors.py' `grep -c '^chr\s' 'circos/conf/karyotype.txt'`
-    > 'circos/conf/karyotype-colors.conf' &&
+    > 'circos/conf/karyotype-colors.conf';
 
-touch circos/conf/karyotype-colors.conf &&
+touch circos/conf/karyotype-colors.conf;
 
 ## #if $ideogram.bands.bands:
 ##     #if $ideogram.bands.convert_bands:
 ##         python '$__tool_directory__/process-cytogenetic-bands.py'
 ##             '${ideogram.bands.bands}'
 ##             >> circos/conf/karyotype.txt
-##             2> circos/conf/karyotype-colors.conf &&
+##             2> circos/conf/karyotype-colors.conf;
 ##     #else
 ##         cat '${ideogram.bands.bands}'
-##             >> circos/conf/karyotype.txt &&
+##             >> circos/conf/karyotype.txt;
 ##     #end if
 ## #end if
 
 #if $plot_options.colour_profile:
     #if str($plot_options.colour_profile) == 'cg':
-        cat '$__tool_directory__/colours/cg.conf' >> circos/conf/karyotype-colors.conf &&
+        cat '$__tool_directory__/colours/cg.conf' >> circos/conf/karyotype-colors.conf;
     #end if
 #end if
 
-cp '$circos_conf' circos/conf/circos.conf &&
-cp '$ticks_conf' circos/conf/ticks.conf &&
-cp '$ideogram_conf' circos/conf/ideogram.conf &&
-cp '$data_conf'  circos/conf/data.conf &&
-cp '$links_conf'  circos/conf/links.conf &&
-cp '$test_case_conf' circos/conf/galaxy_test_case.json &&
+cp '$circos_conf' circos/conf/circos.conf ;
+cp '$ticks_conf' circos/conf/ticks.conf ;
+cp '$ideogram_conf' circos/conf/ideogram.conf ;
+cp '$data_conf'  circos/conf/data.conf ;
+cp '$links_conf'  circos/conf/links.conf ;
+cp '$test_case_conf' circos/conf/galaxy_test_case.json ;
 
 ## 2D Data Plots
 #for $hi, $data in enumerate($sec_tdd.data):
-    cp '${data.plot_format.data_source}' circos/data/data-${hi}.txt &&
+    cp '${data.plot_format.data_source}' circos/data/data-${hi}.txt ;
 #end for
 
 ## Link Tracks
 #for $hi, $data in enumerate($sec_links.data):
-    cp '${data.data_source}' circos/data/links-${hi}.txt &&
+    cp '${data.data_source}' circos/data/links-${hi}.txt ;
 #end for
 
 #if $outputs.tar == "yes"
-    tar -czf circos.tar.gz circos &&
+    tar -czf circos.tar.gz circos ;
 #end if
 
 #if $outputs.svg == "yes" or $outputs.png == "yes":
@@ -617,10 +617,10 @@
         </section>
     </inputs>
     <outputs>
-        <data name="output_png" format="png" from_work_dir="circos.png" label="Circos Plot">
+        <data name="output_png" format="png" from_work_dir="circos.png" label="Circos Plot (PNG)">
             <filter>outputs['png']</filter>
         </data>
-        <data name="output_svg" format="svg" from_work_dir="circos.svg" label="Circos Plot">
+        <data name="output_svg" format="svg" from_work_dir="circos.svg" label="Circos Plot (SVG)">
             <filter>outputs['svg']</filter>
         </data>
         <data name="output_tar" format="tar.gz" from_work_dir="circos.tar.gz" label="Circos Conf Files">
--- a/macros.xml	Mon Nov 22 12:23:12 2021 +0000
+++ b/macros.xml	Wed Apr 12 15:09:05 2023 +0000
@@ -1,21 +1,20 @@
 <?xml version="1.0"?>
 <macros>
   <token name="@TOOL_VERSION@">0.69.8</token>
-  <token name="@VERSION_SUFFIX@">10</token>
+  <token name="@VERSION_SUFFIX@">12</token>
 
   <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy@VERSION_SUFFIX@</token>
 
   <xml name="requirements">
       <requirements>
         <requirement type="package" version="@TOOL_VERSION@">circos</requirement>
-        <requirement type="package" version="2.7">python</requirement>
-        <requirement type="package" version="0.6.4">bcbiogff</requirement>
-        <requirement type="package" version="1.70">biopython</requirement>
-        <requirement type="package" version="0.3.13">pybigwig</requirement>
+        <requirement type="package" version="0.6.6">bcbiogff</requirement>
+        <!-- tiles-from-gff3.py and text-from-gff3.py needs UnknownSeq which is removed in 1.81  -->
+        <requirement type="package" version="1.79">biopython</requirement>
+        <requirement type="package" version="0.3.18">pybigwig</requirement>
         <requirement type="package" version="0.23">circos-tools</requirement>
-        <requirement type="package" version="3.4">grep</requirement>
-        <requirement type="package" version="5.1.0">gawk</requirement>
-        <requirement type="package" version="1.29">tar</requirement>
+        <requirement type="package" version="3.10">grep</requirement>
+        <requirement type="package" version="1.34">tar</requirement>
         <yield />
       </requirements>
   </xml>
--- a/macros_tests.xml	Mon Nov 22 12:23:12 2021 +0000
+++ b/macros_tests.xml	Wed Apr 12 15:09:05 2023 +0000
@@ -23,24 +23,9 @@
                 <section name="reference_genome">
                     <conditional name="ref">
                         <param name="ref_source" value="history" />
-                        <param name="genome_fasta" value="1/input.fa" />
+                        <param name="genome_fasta" value="too-many.fa" />
                     </conditional>
                 </section>
-
-                <section name="outputs">
-                    <param name="png" value="yes" />
-                    <param name="svg" value="yes" />
-                </section>
-
-                <section name="limits">
-                    <param name="max_ticks" value="1" />
-                    <param name="max_ideograms" value="1" />
-                    <param name="max_links" value="1" />
-                    <param name="max_points_per_track" value="1" />
-                </section>
-
-                <output name="output_png" file="0/out.png" compare="sim_size" delta="15000" ftype="png"/>
-                <output name="output_svg" file="0/out.svg" compare="sim_size" delta="15000" ftype="svg"/>
             </test>
 
             <test>
@@ -113,6 +98,36 @@
                 <output name="output_png" file="1/out.png" compare="sim_size" delta="15000" ftype="png"/>
                 <output name="output_svg" file="1/out.svg" compare="sim_size" delta="15000" ftype="svg"/>
             </test>
+            <test>
+                <section name="reference_genome">
+                    <conditional name="ref">
+                        <param name="ref_source" value="history" />
+                        <param name="genome_fasta" value="1/input.fa" />
+                    </conditional>
+                </section>
+
+                <section name="outputs">
+                    <param name="tar" value="yes" />
+                    <param name="png" value="no" />
+                    <param name="svg" value="no" />
+                </section>
+
+                <output name="output_tar" file="2/out.tar" compare="sim_size" delta="15000"/>
+            </test>
+            <test>
+                <section name="reference_genome">
+                    <conditional name="ref">
+                        <param name="ref_source" value="karyotype" />
+                        <param name="input_karyotype" value="3/chrom.tab" />
+                    </conditional>
+                </section>
+
+                <section name="outputs">
+                    <param name="png" value="yes" />
+                </section>
+
+                <output name="output_tar" file="3/out.png" compare="sim_size" delta="15000"/>
+            </test>
         </tests>
     </xml>
 </macros>
--- a/process-cytogenetic-bands.py	Mon Nov 22 12:23:12 2021 +0000
+++ b/process-cytogenetic-bands.py	Wed Apr 12 15:09:05 2023 +0000
@@ -29,7 +29,7 @@
         if line.startswith("#"):
             continue
 
-        lineData = dict(zip(COLS, line.split()))
+        lineData = dict(list(zip(COLS, line.split())))
         color = lineData.get("itemRgb", "gpos50")
 
         if color not in colormap:
@@ -47,7 +47,7 @@
                 # Does not look like an int
                 continue
 
-            colormap[color] = "gx-karyotype-%s" % len(colormap.keys())
+            colormap[color] = "gx-karyotype-%s" % len(list(colormap.keys()))
 
             sys.stderr.write(
                 "{colorName} = {color}\n".format(colorName=colormap[color], color=color)
--- a/stack-histogram.py	Mon Nov 22 12:23:12 2021 +0000
+++ b/stack-histogram.py	Wed Apr 12 15:09:05 2023 +0000
@@ -12,7 +12,7 @@
     bws = [pyBigWig.open(x) for x in files]
 
     # obtain some chroms. Hope all sets are identical!
-    k = bws[0].chroms().keys()
+    k = list(bws[0].chroms().keys())
 
     # do magic?
     # nah.
--- a/stack-histogram.xml	Mon Nov 22 12:23:12 2021 +0000
+++ b/stack-histogram.xml	Wed Apr 12 15:09:05 2023 +0000
@@ -29,7 +29,7 @@
     <tests>
         <test>
             <param name="input" value="scatter/1.bw,scatter/1.bw,scatter/1.bw" ftype="bigwig" />
-            <output name="output" file="scatter/1.multi.out" ftype="tabular" />
+            <output name="output" file="scatter/1.multi.out" ftype="tabular" sort="true"/>
         </test>
     </tests>
     <help><![CDATA[
--- a/tableviewer.xml	Mon Nov 22 12:23:12 2021 +0000
+++ b/tableviewer.xml	Wed Apr 12 15:09:05 2023 +0000
@@ -620,10 +620,10 @@
         <expand macro="limits" />
     </inputs>
     <outputs>
-        <data name="output_png" format="png" from_work_dir="circos.png" label="Circos TableViewer Plot">
+        <data name="output_png" format="png" from_work_dir="circos.png" label="Circos TableViewer Plot (PNG)">
             <filter>outputs['png']</filter>
         </data>
-        <data name="output_svg" format="svg" from_work_dir="circos.svg" label="Circos TableViewer Plot">
+        <data name="output_svg" format="svg" from_work_dir="circos.svg" label="Circos TableViewer Plot (SVG)">
             <filter>outputs['svg']</filter>
         </data>
         <data name="output_tar" format="tar.gz" from_work_dir="circos.tar.gz" label="Circos TableViewer Conf Files">
Binary file test-data/2/out.tar has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3/chrom.tab	Wed Apr 12 15:09:05 2023 +0000
@@ -0,0 +1,24 @@
+chr	-	hs1	1	0	249250621	chr1
+chr	-	hs2	2	0	243199373	chr2
+chr	-	hs3	3	0	198022430	chr3
+chr	-	hs4	4	0	191154276	chr4
+chr	-	hs5	5	0	180915260	chr5
+chr	-	hs6	6	0	171115067	chr6
+chr	-	hs7	7	0	159138663	chr7
+chr	-	hs8	8	0	146364022	chr8
+chr	-	hs9	9	0	141213431	chr9
+chr	-	hs10	10	0	135534747	chr10
+chr	-	hs11	11	0	135006516	chr11
+chr	-	hs12	12	0	133851895	chr12
+chr	-	hs13	13	0	115169878	chr13
+chr	-	hs14	14	0	107349540	chr14
+chr	-	hs15	15	0	102531392	chr15
+chr	-	hs16	16	0	90354753	chr16
+chr	-	hs17	17	0	81195210	chr17
+chr	-	hs18	18	0	78077248	chr18
+chr	-	hs19	19	0	59128983	chr19
+chr	-	hs20	20	0	63025520	chr20
+chr	-	hs21	21	0	48129895	chr21
+chr	-	hs22	22	0	51304566	chr22
+chr	-	hsX	x	0	155270560	chrx
+chr	-	hsY	y	0	59373566	chry
Binary file test-data/3/out.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/too-many.fa	Wed Apr 12 15:09:05 2023 +0000
@@ -0,0 +1,600 @@
+>seq1
+tcga
+>seq2
+tcga
+>seq3
+tcga
+>seq4
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+>seq5
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