# HG changeset patch
# User iuc
# Date 1681312145 0
# Node ID c4bde687c84660ca42726c564e76e76342419e91
# Parent  290a1155998572506e0ac38e520aee1284ff7c76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 0cfd88d16b0b20a66d4b21b037ddee6a8c440d88

diff -r 290a11559985 -r c4bde687c846 circos.xml
--- 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">
diff -r 290a11559985 -r c4bde687c846 macros.xml
--- 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>
diff -r 290a11559985 -r c4bde687c846 macros_tests.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>
diff -r 290a11559985 -r c4bde687c846 process-cytogenetic-bands.py
--- 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)
diff -r 290a11559985 -r c4bde687c846 stack-histogram.py
--- 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.
diff -r 290a11559985 -r c4bde687c846 stack-histogram.xml
--- 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[
diff -r 290a11559985 -r c4bde687c846 tableviewer.xml
--- 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">
diff -r 290a11559985 -r c4bde687c846 test-data/2/out.tar
Binary file test-data/2/out.tar has changed
diff -r 290a11559985 -r c4bde687c846 test-data/3/chrom.tab
--- /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
diff -r 290a11559985 -r c4bde687c846 test-data/3/out.png
Binary file test-data/3/out.png has changed
diff -r 290a11559985 -r c4bde687c846 test-data/too-many.fa
--- /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
+tcga
+>seq5
+tcga
+>seq6
+tcga
+>seq7
+tcga
+>seq8
+tcga
+>seq9
+tcga
+>seq10
+tcga
+>seq11
+tcga
+>seq12
+tcga
+>seq13
+tcga
+>seq14
+tcga
+>seq15
+tcga
+>seq16
+tcga
+>seq17
+tcga
+>seq18
+tcga
+>seq19
+tcga
+>seq20
+tcga
+>seq21
+tcga
+>seq22
+tcga
+>seq23
+tcga
+>seq24
+tcga
+>seq25
+tcga
+>seq26
+tcga
+>seq27
+tcga
+>seq28
+tcga
+>seq29
+tcga
+>seq30
+tcga
+>seq31
+tcga
+>seq32
+tcga
+>seq33
+tcga
+>seq34
+tcga
+>seq35
+tcga
+>seq36
+tcga
+>seq37
+tcga
+>seq38
+tcga
+>seq39
+tcga
+>seq40
+tcga
+>seq41
+tcga
+>seq42
+tcga
+>seq43
+tcga
+>seq44
+tcga
+>seq45
+tcga
+>seq46
+tcga
+>seq47
+tcga
+>seq48
+tcga
+>seq49
+tcga
+>seq50
+tcga
+>seq51
+tcga
+>seq52
+tcga
+>seq53
+tcga
+>seq54
+tcga
+>seq55
+tcga
+>seq56
+tcga
+>seq57
+tcga
+>seq58
+tcga
+>seq59
+tcga
+>seq60
+tcga
+>seq61
+tcga
+>seq62
+tcga
+>seq63
+tcga
+>seq64
+tcga
+>seq65
+tcga
+>seq66
+tcga
+>seq67
+tcga
+>seq68
+tcga
+>seq69
+tcga
+>seq70
+tcga
+>seq71
+tcga
+>seq72
+tcga
+>seq73
+tcga
+>seq74
+tcga
+>seq75
+tcga
+>seq76
+tcga
+>seq77
+tcga
+>seq78
+tcga
+>seq79
+tcga
+>seq80
+tcga
+>seq81
+tcga
+>seq82
+tcga
+>seq83
+tcga
+>seq84
+tcga
+>seq85
+tcga
+>seq86
+tcga
+>seq87
+tcga
+>seq88
+tcga
+>seq89
+tcga
+>seq90
+tcga
+>seq91
+tcga
+>seq92
+tcga
+>seq93
+tcga
+>seq94
+tcga
+>seq95
+tcga
+>seq96
+tcga
+>seq97
+tcga
+>seq98
+tcga
+>seq99
+tcga
+>seq100
+tcga
+>seq101
+tcga
+>seq102
+tcga
+>seq103
+tcga
+>seq104
+tcga
+>seq105
+tcga
+>seq106
+tcga
+>seq107
+tcga
+>seq108
+tcga
+>seq109
+tcga
+>seq110
+tcga
+>seq111
+tcga
+>seq112
+tcga
+>seq113
+tcga
+>seq114
+tcga
+>seq115
+tcga
+>seq116
+tcga
+>seq117
+tcga
+>seq118
+tcga
+>seq119
+tcga
+>seq120
+tcga
+>seq121
+tcga
+>seq122
+tcga
+>seq123
+tcga
+>seq124
+tcga
+>seq125
+tcga
+>seq126
+tcga
+>seq127
+tcga
+>seq128
+tcga
+>seq129
+tcga
+>seq130
+tcga
+>seq131
+tcga
+>seq132
+tcga
+>seq133
+tcga
+>seq134
+tcga
+>seq135
+tcga
+>seq136
+tcga
+>seq137
+tcga
+>seq138
+tcga
+>seq139
+tcga
+>seq140
+tcga
+>seq141
+tcga
+>seq142
+tcga
+>seq143
+tcga
+>seq144
+tcga
+>seq145
+tcga
+>seq146
+tcga
+>seq147
+tcga
+>seq148
+tcga
+>seq149
+tcga
+>seq150
+tcga
+>seq151
+tcga
+>seq152
+tcga
+>seq153
+tcga
+>seq154
+tcga
+>seq155
+tcga
+>seq156
+tcga
+>seq157
+tcga
+>seq158
+tcga
+>seq159
+tcga
+>seq160
+tcga
+>seq161
+tcga
+>seq162
+tcga
+>seq163
+tcga
+>seq164
+tcga
+>seq165
+tcga
+>seq166
+tcga
+>seq167
+tcga
+>seq168
+tcga
+>seq169
+tcga
+>seq170
+tcga
+>seq171
+tcga
+>seq172
+tcga
+>seq173
+tcga
+>seq174
+tcga
+>seq175
+tcga
+>seq176
+tcga
+>seq177
+tcga
+>seq178
+tcga
+>seq179
+tcga
+>seq180
+tcga
+>seq181
+tcga
+>seq182
+tcga
+>seq183
+tcga
+>seq184
+tcga
+>seq185
+tcga
+>seq186
+tcga
+>seq187
+tcga
+>seq188
+tcga
+>seq189
+tcga
+>seq190
+tcga
+>seq191
+tcga
+>seq192
+tcga
+>seq193
+tcga
+>seq194
+tcga
+>seq195
+tcga
+>seq196
+tcga
+>seq197
+tcga
+>seq198
+tcga
+>seq199
+tcga
+>seq200
+tcga
+>seq201
+tcga
+>seq202
+tcga
+>seq203
+tcga
+>seq204
+tcga
+>seq205
+tcga
+>seq206
+tcga
+>seq207
+tcga
+>seq208
+tcga
+>seq209
+tcga
+>seq210
+tcga
+>seq211
+tcga
+>seq212
+tcga
+>seq213
+tcga
+>seq214
+tcga
+>seq215
+tcga
+>seq216
+tcga
+>seq217
+tcga
+>seq218
+tcga
+>seq219
+tcga
+>seq220
+tcga
+>seq221
+tcga
+>seq222
+tcga
+>seq223
+tcga
+>seq224
+tcga
+>seq225
+tcga
+>seq226
+tcga
+>seq227
+tcga
+>seq228
+tcga
+>seq229
+tcga
+>seq230
+tcga
+>seq231
+tcga
+>seq232
+tcga
+>seq233
+tcga
+>seq234
+tcga
+>seq235
+tcga
+>seq236
+tcga
+>seq237
+tcga
+>seq238
+tcga
+>seq239
+tcga
+>seq240
+tcga
+>seq241
+tcga
+>seq242
+tcga
+>seq243
+tcga
+>seq244
+tcga
+>seq245
+tcga
+>seq246
+tcga
+>seq247
+tcga
+>seq248
+tcga
+>seq249
+tcga
+>seq250
+tcga
+>seq251
+tcga
+>seq252
+tcga
+>seq253
+tcga
+>seq254
+tcga
+>seq255
+tcga
+>seq256
+tcga
+>seq257
+tcga
+>seq258
+tcga
+>seq259
+tcga
+>seq260
+tcga
+>seq261
+tcga
+>seq262
+tcga
+>seq263
+tcga
+>seq264
+tcga
+>seq265
+tcga
+>seq266
+tcga
+>seq267
+tcga
+>seq268
+tcga
+>seq269
+tcga
+>seq270
+tcga
+>seq271
+tcga
+>seq272
+tcga
+>seq273
+tcga
+>seq274
+tcga
+>seq275
+tcga
+>seq276
+tcga
+>seq277
+tcga
+>seq278
+tcga
+>seq279
+tcga
+>seq280
+tcga
+>seq281
+tcga
+>seq282
+tcga
+>seq283
+tcga
+>seq284
+tcga
+>seq285
+tcga
+>seq286
+tcga
+>seq287
+tcga
+>seq288
+tcga
+>seq289
+tcga
+>seq290
+tcga
+>seq291
+tcga
+>seq292
+tcga
+>seq293
+tcga
+>seq294
+tcga
+>seq295
+tcga
+>seq296
+tcga
+>seq297
+tcga
+>seq298
+tcga
+>seq299
+tcga
+>seq300
+tcga