Mercurial > repos > fubar > jbrowse2
diff x/galaxy.xml @ 127:fbabf7498471 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 116b1a4bbd62251ad552306df2dc8aa8f46c6721
| author | fubar |
|---|---|
| date | Mon, 07 Oct 2024 02:11:55 +0000 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/x/galaxy.xml Mon Oct 07 02:11:55 2024 +0000 @@ -0,0 +1,628 @@ +<?xml version="1.0"?> +<root> + <metadata> + <general> + <defaultLocation></defaultLocation> + <zipOut>true</zipOut> + <bpPerPx>50</bpPerPx> + <analytics>false</analytics> + <primary_color>#0d233f</primary_color> + <secondary_color>#721e63</secondary_color> + <tertiary_color>#135560</tertiary_color> + <quaternary_color>#ffb11d</quaternary_color> + <font_size>10</font_size> + <session_name>New test session</session_name> + </general> + <galaxyUrl>http://localhost:8080</galaxyUrl> + </metadata> + <assembly> + <metadata> + <genomes> + <genome path="/tmp/tmpus622kw5/files/7/4/8/dataset_748d2461-ea0f-4e92-b129-e680b76d4c81.dat" label="Merlin" useuri="no"> + <metadata> + + <dataset id="801225f8dc4ca2f7" + hid="1" + size="171.6 KB" + edam_format="format_1929" + file_ext="fasta" + dname = "Merlin" + /> + <history + user_email="planemo@galaxyproject.org" + user_id="1" + display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/> + id="801225f8dc4ca2f7" + /> + <metadata + dbkey="?" + data_lines="2881" + sequences="1" + /> + <tool + tool_id="upload1" + tool_version="1.1.7" + /> + </metadata> + </genome> + </genomes> + </metadata> + <tracks> + <track cat="Assembly properties" format="gff" visibility="default_on"> + <files> + <trackFile path="/tmp/tmpus622kw5/files/b/7/d/dataset_b7de2a4d-8123-493d-99ad-6f251912ae1c.dat" ext="gff3" label="merlin.gff3" useuri="no"> + <metadata> + <dataset id="f899122287bdd0b2" hid="2" + size="5.0 KB" + edam_format="format_1975" + file_ext="gff3" /> + <history id="801225f8dc4ca2f7" + user_email="planemo@galaxyproject.org" + user_id="1" + display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/> + <metadata + dbkey="?" + data_lines="9" + comment_lines="10" + columns="9" + column_names="[]" + delimiter="__tc__" + attributes="23" + /> + <tool + tool_id="upload1" + tool_version="1.1.7" + /> + </metadata> + </trackFile> + </files> + <options> + <style> + <type>LinearBasicDisplay</type> + <trackShowLabels>false</trackShowLabels> + <trackShowDescriptions>false</trackShowDescriptions> + </style> + <gff> + </gff> + </options> + </track> + <track cat="Assembly properties" format="bigwig" visibility="default_on"> + <files> + <trackFile path="/tmp/tmpus622kw5/files/b/5/2/dataset_b523b4bc-c4b6-4eb0-a914-364fb4f91db4.dat" ext="bigwig" label="merlin.bw" useuri="no"> + <metadata> + <dataset id="78cc944b7b4634f8" hid="3" + size="81.6 KB" + edam_format="format_3006" + file_ext="bigwig" /> + <history id="801225f8dc4ca2f7" + user_email="planemo@galaxyproject.org" + user_id="1" + display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/> + <metadata + dbkey="?" + /> + <tool + tool_id="upload1" + tool_version="1.1.7" + /> + </metadata> + </trackFile> + </files> + <options> + <style> + <type>LinearWiggleDisplay</type> + <color>#135560</color> + <autoscale>globalsd</autoscale> + <resolution>1</resolution> + <summaryScoreMode>whiskers</summaryScoreMode> + <filled>true</filled> + <scaleType>linear</scaleType> + <displayCrossHatches>true</displayCrossHatches> + <minScore></minScore> + <maxScore></maxScore> + </style> + </options> + </track> + <track cat="Assembly properties" format="bed" visibility="default_on"> + <files> + <trackFile path="/tmp/tmpus622kw5/files/b/1/3/dataset_b132250a-57b0-4f00-a94b-be3b7b14fa98.dat" ext="bed" label="test-6.bed" useuri="no"> + <metadata> + <dataset id="3628324a9a091ab7" hid="4" + size="180 bytes" + edam_format="format_3003" + file_ext="bed" /> + <history id="801225f8dc4ca2f7" + user_email="planemo@galaxyproject.org" + user_id="1" + display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/> + <metadata + dbkey="?" + data_lines="3" + comment_lines="0" + columns="6" + column_names="[]" + delimiter="__tc__" + chromCol="1" + startCol="2" + endCol="3" + strandCol="6" + viz_filter_cols="[4]" + /> + <tool + tool_id="upload1" + tool_version="1.1.7" + /> + </metadata> + </trackFile> + </files> + <options> + <style> + <type>LinearBasicDisplay</type> + <trackShowLabels>false</trackShowLabels> + <trackShowDescriptions>false</trackShowDescriptions> + </style> + <bed> + <usebedscore>false</usebedscore> + </bed> + </options> + </track> + <track cat="Assembly properties" format="vcf" visibility="default_on"> + <files> + <trackFile path="/tmp/tmpus622kw5/files/4/9/6/dataset_49609184-5279-4c15-8e1a-b492552a02ff.dat" ext="vcf" label="merlin.vcf" useuri="no"> + <metadata> + <dataset id="7e78e1a21bf444fa" hid="5" + size="1.5 KB" + edam_format="format_3016" + file_ext="vcf" /> + <history id="801225f8dc4ca2f7" + user_email="planemo@galaxyproject.org" + user_id="1" + display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/> + <metadata + dbkey="?" + data_lines="5" + comment_lines="18" + columns="12" + column_names="[]" + delimiter="__tc__" + viz_filter_cols="[5]" + sample_names="[NA00001,NA00002,NA00003]" + /> + <tool + tool_id="upload1" + tool_version="1.1.7" + /> + </metadata> + </trackFile> + </files> + <options> + <style> + <type>LinearVariantDisplay</type> + <trackShowLabels>false</trackShowLabels> + <trackShowDescriptions>false</trackShowDescriptions> + </style> + </options> + </track> + <track cat="Assembly properties" format="cram" visibility="default_on"> + <files> + <trackFile path="/tmp/tmpus622kw5/files/8/6/5/dataset_86597dfb-d461-4ef9-9eb6-c8262351f18c.dat" ext="cram" label="merlin.cram" useuri="no"> + <metadata> + <dataset id="80ac834e53a3892f" hid="6" + size="10.9 KB" + edam_format="format_3462" + file_ext="cram" /> + <history id="801225f8dc4ca2f7" + user_email="planemo@galaxyproject.org" + user_id="1" + display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/> + <metadata + dbkey="?" + cram_version="3.0" + cram_index="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX" + /> + <tool + tool_id="upload1" + tool_version="1.1.7" + /> + </metadata> + </trackFile> + </files> + <options> + <style> + <type>LinearAlignmentsDisplay</type> + </style> + <cram> + <cram_index> + /tmp/tmpus622kw5/files/8/6/5/dataset_86597dfb-d461-4ef9-9eb6-c8262351f18c.dat ~ /tmp/tmpus622kw5/files/_metadata_files/c/d/8/metadata_cd855eb8-90c3-478b-af5d-47ba048c1765.dat, + </cram_index> + </cram> + </options> + </track> + <track cat="Assembly properties" format="bam" visibility="default_on"> + <files> + <trackFile path="/tmp/tmpus622kw5/files/d/6/8/dataset_d6878dfb-6c11-4673-a348-d7c441e5c7db.dat" ext="bam" label="merlin-sample.bam" useuri="no"> + <metadata> + <dataset id="64ba8fadcb1fc688" hid="7" + size="13.0 KB" + edam_format="format_2572" + file_ext="bam" /> + <history id="801225f8dc4ca2f7" + user_email="planemo@galaxyproject.org" + user_id="1" + display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/> + <metadata + dbkey="?" + columns="12" + column_names="[QNAME,FLAG,RNAME,POS,MAPQ,CIGAR,MRNM,MPOS,ISIZE,SEQ,QUAL,OPT]" + bam_version="1.3" + sort_order="coordinate" + read_groups="[]" + reference_names="[Merlin]" + reference_lengths="[172788]" + bam_index="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX" + /> + <tool + tool_id="upload1" + tool_version="1.1.7" + /> + </metadata> + </trackFile> + </files> + <options> + <style> + <type>LinearAlignmentsDisplay</type> + </style> + <bam> + <bam_index> + /tmp/tmpus622kw5/files/d/6/8/dataset_d6878dfb-6c11-4673-a348-d7c441e5c7db.dat ~ /tmp/tmpus622kw5/files/_metadata_files/8/9/f/metadata_89f41037-55f2-4252-9884-5eba8bd4e748.dat, + </bam_index> + </bam> + </options> + </track> + <track cat="Assembly properties" format="maf" visibility="default_on"> + <files> + <trackFile path="/tmp/tmpus622kw5/files/f/e/c/dataset_feca1abe-d55a-4ade-a506-1e1f99e76cb3.dat" ext="maf" label="merlinlastz.maf" useuri="no"> + <metadata> + <dataset id="d64497191f3f5d7f" hid="8" + size="1.5 KB" + edam_format="format_3008" + file_ext="maf" /> + <history id="801225f8dc4ca2f7" + user_email="planemo@galaxyproject.org" + user_id="1" + display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/> + <metadata + dbkey="?" + data_lines="0" + species="[Merlin,Merlin1,Merlin2,Merlin3,Merlin4,Merlin5,Merlin6]" + blocks="6" + species_chromosomes="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX" + maf_index="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX" + /> + <tool + tool_id="upload1" + tool_version="1.1.7" + /> + </metadata> + </trackFile> + </files> + <options> + <style> + <type>LinearBasicDisplay</type> + <trackShowLabels>false</trackShowLabels> + <trackShowDescriptions>false</trackShowDescriptions> + </style> + </options> + </track> + <track cat="Assembly properties" format="blastxml" visibility="default_on"> + <files> + <trackFile path="/tmp/tmpus622kw5/files/3/6/5/dataset_365aaf8d-17be-44d6-93c7-dc4952ef511b.dat" ext="blastxml" label="merlin.blastxml" useuri="no"> + <metadata> + <dataset id="3a8027169fd7c75d" hid="9" + size="1.6 MB" + edam_format="format_3331" + file_ext="blastxml" /> + <history id="801225f8dc4ca2f7" + user_email="planemo@galaxyproject.org" + user_id="1" + display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/> + <metadata + dbkey="?" + data_lines="20455" + /> + <tool + tool_id="upload1" + tool_version="1.1.7" + /> + </metadata> + </trackFile> + </files> + <options> + <style> + <type>LinearBasicDisplay</type> + <trackShowLabels>false</trackShowLabels> + <trackShowDescriptions>false</trackShowDescriptions> + </style> + <blast> + <parent>None</parent> + <protein>false</protein> + <min_gap>10</min_gap> + </blast> + </options> + </track> + <track cat="Assembly properties" format="bam" visibility="default_on"> + <files> + <trackFile path="/tmp/tmpus622kw5/files/c/d/9/dataset_cd94dba1-9bb2-4c84-ba3b-a9b269faf031.dat" ext="zip" label="files_0Xfile_data" useuri="no"> + <metadata> + <dataset id="df6e27cbb08754e3" hid="10" + size="275.3 KB" + edam_format="format_2333" + file_ext="zip" /> + <history id="801225f8dc4ca2f7" + user_email="planemo@galaxyproject.org" + user_id="1" + display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/> + <metadata + dbkey="?" + /> + <tool + tool_id="upload1" + tool_version="1.1.7" + /> + </metadata> + </trackFile> + </files> + <options> + <style> + <type>LinearAlignmentsDisplay</type> + </style> + <bam> + <bam_index> + /tmp/tmpus622kw5/files/c/d/9/dataset_cd94dba1-9bb2-4c84-ba3b-a9b269faf031.dat ~ , + </bam_index> + </bam> + </options> + </track> + </tracks> + </assembly> + <assembly> + <metadata> + <genomes> + <genome path="/tmp/tmpus622kw5/files/a/e/2/dataset_ae2fbecc-5b2d-4783-9ff9-dc4c0827a344.dat" label="dm3.fa" useuri="no"> + <metadata> + + <dataset id="47bf7b7c957123a5" + hid="11" + size="27.2 MB" + edam_format="format_1929" + file_ext="fasta" + dname = "dm3.fa" + /> + <history + user_email="planemo@galaxyproject.org" + user_id="1" + display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/> + id="801225f8dc4ca2f7" + /> + <metadata + dbkey="?" + data_lines="401577" + sequences="1" + /> + <tool + tool_id="upload1" + tool_version="1.1.7" + /> + </metadata> + </genome> + </genomes> + </metadata> + <tracks> + <track cat="Assembly properties" format="cool" visibility="default_on"> + <files> + <trackFile path="/tmp/tmpus622kw5/files/5/2/8/dataset_528eb872-92fa-4d06-bda9-b8c3522f6b50.dat" ext="cool" label="dm3test.cool" useuri="no"> + <metadata> + <dataset id="b78501a0735fb2a5" hid="12" + size="250.1 KB" + edam_format="format_3590" + file_ext="cool" /> + <history id="801225f8dc4ca2f7" + user_email="planemo@galaxyproject.org" + user_id="1" + display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/> + <metadata + dbkey="?" + /> + <tool + tool_id="upload1" + tool_version="1.1.7" + /> + </metadata> + </trackFile> + </files> + <options> + <style> + <type>LinearHicDisplay</type> + </style> + <cool> + </cool> + </options> + </track> + </tracks> + </assembly> + <assembly> + <metadata> + <genomes> + <genome path="/tmp/tmpus622kw5/files/a/d/d/dataset_add7c5ef-1f3d-4c73-9d9c-43892361ebfe.dat" label="Ppersica1.fa" useuri="no"> + <metadata> + + <dataset id="1cd311606732130f" + hid="13" + size="46.2 MB" + edam_format="format_1929" + file_ext="fasta" + dname = "Ppersica1.fa" + /> + <history + user_email="planemo@galaxyproject.org" + user_id="1" + display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/> + id="801225f8dc4ca2f7" + /> + <metadata + dbkey="?" + data_lines="598142" + sequences="1" + /> + <tool + tool_id="upload1" + tool_version="1.1.7" + /> + </metadata> + </genome> + </genomes> + </metadata> + <tracks> + <track cat="Assembly properties" format="paf" visibility="default_on"> + <files> + <trackFile path="/tmp/tmpus622kw5/files/3/9/6/dataset_396ed6d5-d81e-4a2e-b566-1b69cf0a8ec0.dat" ext="paf" label="peach-grape-map.paf" useuri="no"> + <metadata> + <dataset id="4a3497682f135c57" hid="14" + size="1.1 MB" + edam_format="format_2330" + file_ext="paf" /> + <history id="801225f8dc4ca2f7" + user_email="planemo@galaxyproject.org" + user_id="1" + display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/> + <metadata + dbkey="?" + data_lines="9291" + /> + <tool + tool_id="upload1" + tool_version="1.1.7" + /> + </metadata> + </trackFile> + </files> + <options> + <style> + </style> + <paf> + <genome> + /tmp/tmpus622kw5/files/e/4/4/dataset_e44ca09b-d9ff-4a99-a4cb-e50f24a66ff9.dat ~ Vvinifera1.fa, + </genome> + <useuri> + false + </useuri> + </paf> + </options> + </track> + <track cat="Assembly properties" format="paf" visibility="default_on"> + <files> + <trackFile path="/tmp/tmpus622kw5/files/2/7/2/dataset_272188a9-0367-4677-9b28-ad5e84aceb99.dat" ext="paf" label="arabgrapepeach.paf" useuri="no"> + <metadata> + <dataset id="edaefaa2c8238b09" hid="16" + size="12.8 MB" + edam_format="format_2330" + file_ext="paf" /> + <history id="801225f8dc4ca2f7" + user_email="planemo@galaxyproject.org" + user_id="1" + display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/> + <metadata + dbkey="?" + data_lines="129777" + /> + <tool + tool_id="upload1" + tool_version="1.1.7" + /> + </metadata> + </trackFile> + </files> + <options> + <style> + </style> + <paf> + <genome> + https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa.gz ~ arabidopsis.URI, + https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa.gz ~ Vvinifera1.URI, + </genome> + <useuri> + true + </useuri> + </paf> + </options> + </track> + <track cat="Assembly properties" format="paf" visibility="default_on"> + <files> + <trackFile path="/tmp/tmpus622kw5/files/2/7/2/dataset_272188a9-0367-4677-9b28-ad5e84aceb99.dat" ext="paf" label="arabgrapepeach.paf" useuri="no"> + <metadata> + <dataset id="edaefaa2c8238b09" hid="16" + size="12.8 MB" + edam_format="format_2330" + file_ext="paf" /> + <history id="801225f8dc4ca2f7" + user_email="planemo@galaxyproject.org" + user_id="1" + display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/> + <metadata + dbkey="?" + data_lines="129777" + /> + <tool + tool_id="upload1" + tool_version="1.1.7" + /> + </metadata> + </trackFile> + </files> + <options> + <style> + </style> + <paf> + <genome> + /tmp/tmpus622kw5/files/e/4/4/dataset_e44ca09b-d9ff-4a99-a4cb-e50f24a66ff9.dat ~ Vvinifera1.fa, + </genome> + <useuri> + false + </useuri> + </paf> + </options> + </track> + </tracks> + </assembly> + <assembly> + <metadata> + <genomes> + <genome path="https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz" label="hg38" useuri="yes"> + <metadata> + <dataset + dname = "hg38" /> + </metadata> + </genome> + </genomes> + </metadata> + <tracks> + <track cat="Assembly properties" format="hic" visibility="default_on"> + <files> + <trackFile path="https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic" ext="hic" + label="humanhic" useuri="yes"> + <metadata> + <dataset id = "https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic" /> + </metadata> + </trackFile> + </files> + <options> + <style> + <type>LinearHicDisplay</type> + </style> + <hic> + </hic> + </options> + </track> + </tracks> + </assembly> +</root>