| Previous changeset 35:15da358c3108 (2024-02-28) Next changeset 37:7adde511daa1 (2024-02-29) |
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Commit message:
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty |
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modified:
autogenJB2.py autogenJB2.xml jbrowse2.xml |
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added:
__pycache__/jbrowse2.cpython-310.pyc |
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| diff -r 15da358c3108 -r 5f39f745682f __pycache__/jbrowse2.cpython-310.pyc |
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| Binary file __pycache__/jbrowse2.cpython-310.pyc has changed |
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| diff -r 15da358c3108 -r 5f39f745682f autogenJB2.py --- a/autogenJB2.py Wed Feb 28 10:08:57 2024 +0000 +++ b/autogenJB2.py Thu Feb 29 00:47:58 2024 +0000 |
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| @@ -109,9 +109,9 @@ } } elif trext == 'bam': - track_conf["conf"] = {"options": {"bam": {"bam_indices": {"bam_index": track[3]}}}} + track_conf = {"conf": {"options": {"bam": {"bam_indices": {"bam_index": track[3]}}}}} elif trext == 'cram': - track_conf["conf"] = {"options": {"cram": {"cram_indices": {"cram_index": track[3]}}}} + track_conf = {"conf": {"options": {"cram": {"cram_indices": {"cram_index": track[3]}}}}} else: track_conf = {} track_conf["format"] = trext |
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| diff -r 15da358c3108 -r 5f39f745682f autogenJB2.xml --- a/autogenJB2.xml Wed Feb 28 10:08:57 2024 +0000 +++ b/autogenJB2.xml Thu Feb 29 00:47:58 2024 +0000 |
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| @@ -1,4 +1,4 @@ - <tool id="autogenjb2" name="autogenjb2" version="2.10.2_0" profile="22.05"> + <tool id="autogenjb2" name="autogenjb2" version="2.10.2.0" profile="22.05"> <description>Track collection to JBrowse2</description> <macros> <import>macros.xml</import> @@ -26,10 +26,10 @@ --sessName "Autogen JBrowse" && cp '$output.files_path/index.html' '$output' - ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph. - - +#if str($uglyTestingHack) == "enabled": + && cp '$output.files_path/config.json' '$output' +#end if ]]></command> <inputs> <param @@ -37,11 +37,31 @@ name="autoCollection" type="data_collection"> </param> + <param type="hidden" name="uglyTestingHack" value="" /> </inputs> <outputs> <data format="html" name="output" label="AutoJBrowse2"/> </outputs> +<tests> + <test> + <param name="uglyTestingHack" value="enabled" /> + <param name="autoCollection"> + <collection type="list"> + <element name="Merlin" value="merlin.fa" ftype="fasta"/> + <element name="merlin-sample.bam" value="bam/merlin-sample.bam" ftype="bam"/> + </collection> + </param> + <output name="output"> + <assert_contents> + <has_text text='"name": "Merlin",'/> + <has_text text='"name": "merlin-sample.bam",'/> + <has_text text='"uri": "Merlin.fa.gz.fai"'/> + <has_text text='"uri": "bam_0_merlin-sample.bam.bam.bai"'/> + </assert_contents> + </output> + </test> +</tests> <help><![CDATA[ JBrowse2-in-Galaxy |
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| diff -r 15da358c3108 -r 5f39f745682f jbrowse2.xml --- a/jbrowse2.xml Wed Feb 28 10:08:57 2024 +0000 +++ b/jbrowse2.xml Thu Feb 29 00:47:58 2024 +0000 |
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| @@ -140,11 +140,11 @@ <options> #if str($track.data_format.data_format_select) == "bam": - <pileup> + <bam> #for $dataset in $track.data_format.annotation: <bam_index>${dataset.metadata.bam_index}</bam_index> #end for - </pileup> + </bam> #else if str($track.data_format.data_format_select) == "cram": <cram> <cram_indices> |