| Previous changeset 10:7f13dc906cb9 (2021-10-11) Next changeset 12:290a11559985 (2021-11-22) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit b9ec351920dbc83fa14bd1f8cfdd0a6a19b89473" |
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modified:
alignments-to-links.xml bundlelinks.xml circos.xml gc_skew.xml macros.xml resample.xml scatter-from-wiggle.xml stack-histogram.xml text-from-interval.xml tiles-from-interval.xml |
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| diff -r 7f13dc906cb9 -r 31a35811dda6 alignments-to-links.xml --- a/alignments-to-links.xml Mon Oct 11 10:09:51 2021 +0000 +++ b/alignments-to-links.xml Tue Nov 16 09:20:08 2021 +0000 |
| [ |
| @@ -4,8 +4,6 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - </expand> <edam_topics> <edam_topic>topic_0797</edam_topic> <edam_topic>topic_0092</edam_topic> @@ -13,6 +11,8 @@ <edam_operations> <edam_operation>operation_1812</edam_operation> </edam_operations> + <expand macro="requirements"> + </expand> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/alignments-to-links.py' '$input' '$input.ext' > '$output' ]]></command> |
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| diff -r 7f13dc906cb9 -r 31a35811dda6 bundlelinks.xml --- a/bundlelinks.xml Mon Oct 11 10:09:51 2021 +0000 +++ b/bundlelinks.xml Tue Nov 16 09:20:08 2021 +0000 |
| [ |
| @@ -4,7 +4,6 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> <edam_topics> <edam_topic>topic_0797</edam_topic> <edam_topic>topic_0092</edam_topic> @@ -12,6 +11,7 @@ <edam_operations> <edam_operation>operation_3436</edam_operation> </edam_operations> + <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ bundlelinks #if $max_gap: |
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| diff -r 7f13dc906cb9 -r 31a35811dda6 circos.xml --- a/circos.xml Mon Oct 11 10:09:51 2021 +0000 +++ b/circos.xml Tue Nov 16 09:20:08 2021 +0000 |
| [ |
| @@ -11,7 +11,6 @@ <import>macros_conffiles.xml</import> <import>macros_tests.xml</import> </macros> - <expand macro="requirements"/> <edam_topics> <edam_topic>topic_0797</edam_topic> <edam_topic>topic_0092</edam_topic> @@ -19,7 +18,7 @@ <edam_operations> <edam_operation>operation_0337</edam_operation> </edam_operations> - <version_command>circos --version</version_command> + <expand macro="requirements"/> <stdio> <!-- Anything other than zero is an error --> <exit_code range="1:"/> @@ -27,6 +26,7 @@ <!-- In case the return code has not been set propery check stderr too --> <regex match="Circos::Error::fatal_error.* called at"/> </stdio> + <version_command>circos --version</version_command> <command><![CDATA[ ## Directory structure mkdir -p circos/conf/ circos/data/ && @@ -58,7 +58,7 @@ genomeref.fa > 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'` |
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| diff -r 7f13dc906cb9 -r 31a35811dda6 gc_skew.xml --- a/gc_skew.xml Mon Oct 11 10:09:51 2021 +0000 +++ b/gc_skew.xml Tue Nov 16 09:20:08 2021 +0000 |
| [ |
| @@ -4,8 +4,6 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - </expand> <edam_topics> <edam_topic>topic_0797</edam_topic> <edam_topic>topic_0092</edam_topic> @@ -13,6 +11,8 @@ <edam_operations> <edam_operation>operation_0262</edam_operation> </edam_operations> + <expand macro="requirements"> + </expand> <command detect_errors="exit_code"><![CDATA[ ln -s -f #if $reference_genome.reference_genome_source == "history" |
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| diff -r 7f13dc906cb9 -r 31a35811dda6 macros.xml --- a/macros.xml Mon Oct 11 10:09:51 2021 +0000 +++ b/macros.xml Tue Nov 16 09:20:08 2021 +0000 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">0.69.8</token> - <token name="@VERSION_SUFFIX@">8</token> + <token name="@VERSION_SUFFIX@">9</token> <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy@VERSION_SUFFIX@</token> |
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| diff -r 7f13dc906cb9 -r 31a35811dda6 resample.xml --- a/resample.xml Mon Oct 11 10:09:51 2021 +0000 +++ b/resample.xml Tue Nov 16 09:20:08 2021 +0000 |
| [ |
| @@ -4,7 +4,6 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> <edam_topics> <edam_topic>topic_0797</edam_topic> <edam_topic>topic_0092</edam_topic> @@ -12,6 +11,7 @@ <edam_operations> <edam_operation>operation_3436</edam_operation> </edam_operations> + <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ resample -bin '$bins' |
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| diff -r 7f13dc906cb9 -r 31a35811dda6 scatter-from-wiggle.xml --- a/scatter-from-wiggle.xml Mon Oct 11 10:09:51 2021 +0000 +++ b/scatter-from-wiggle.xml Tue Nov 16 09:20:08 2021 +0000 |
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| @@ -4,8 +4,6 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - </expand> <edam_topics> <edam_topic>topic_0797</edam_topic> <edam_topic>topic_0092</edam_topic> @@ -13,6 +11,7 @@ <edam_operations> <edam_operation>operation_3434</edam_operation> </edam_operations> + <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/scatter-from-wiggle.py' '$input' > '$output' ]]></command> |
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| diff -r 7f13dc906cb9 -r 31a35811dda6 stack-histogram.xml --- a/stack-histogram.xml Mon Oct 11 10:09:51 2021 +0000 +++ b/stack-histogram.xml Tue Nov 16 09:20:08 2021 +0000 |
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| @@ -4,8 +4,6 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - </expand> <edam_topics> <edam_topic>topic_0797</edam_topic> <edam_topic>topic_0092</edam_topic> @@ -13,6 +11,7 @@ <edam_operations> <edam_operation>operation_0335</edam_operation> </edam_operations> + <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/stack-histogram.py' |
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| diff -r 7f13dc906cb9 -r 31a35811dda6 text-from-interval.xml --- a/text-from-interval.xml Mon Oct 11 10:09:51 2021 +0000 +++ b/text-from-interval.xml Tue Nov 16 09:20:08 2021 +0000 |
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| @@ -4,8 +4,6 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - </expand> <edam_topics> <edam_topic>topic_0797</edam_topic> <edam_topic>topic_0092</edam_topic> @@ -13,6 +11,7 @@ <edam_operations> <edam_operation>operation_3434</edam_operation> </edam_operations> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ python #if $ref.ref_source == 'gff3': |
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| diff -r 7f13dc906cb9 -r 31a35811dda6 tiles-from-interval.xml --- a/tiles-from-interval.xml Mon Oct 11 10:09:51 2021 +0000 +++ b/tiles-from-interval.xml Tue Nov 16 09:20:08 2021 +0000 |
| [ |
| @@ -4,8 +4,6 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - </expand> <edam_topics> <edam_topic>topic_0797</edam_topic> <edam_topic>topic_0092</edam_topic> @@ -13,6 +11,7 @@ <edam_operations> <edam_operation>operation_3434</edam_operation> </edam_operations> + <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ python #if $ref.ref_source == 'gff3': |