| Previous changeset 21:81804a978fc0 (2022-05-07) Next changeset 23:77402759b866 (2022-07-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc |
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modified:
pangolin.xml |
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| diff -r 81804a978fc0 -r a2099fb98cdb pangolin.xml --- a/pangolin.xml Sat May 07 19:52:10 2022 +0000 +++ b/pangolin.xml Fri Jul 08 08:33:57 2022 +0000 |
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| b'@@ -1,70 +1,188 @@\n-<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy2" profile="20.01">\n+<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">\n <description>Phylogenetic Assignment of Outbreak Lineages</description>\n <macros>\n- <token name="@TOOL_VERSION@">4.0.5</token>\n+ <token name="@TOOL_VERSION@">4.1.1</token>\n+ <token name="@PANGOLIN_DATA_VERSION@">1.11</token>\n+ <token name="@CONSTELLATIONS_VERSION@">0.1.10</token>\n+ <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@">4</token>\n+ <!-- a regex describing the scorpio versions that this wrapper version\n+ is backwards-compatible with; can be used with the min_scorpio_version\n+ column of the constellations data table to offer only compatible\n+ versions of constellations data. -->\n+ <token name="@COMPATIBLE_SCORPIO_DATA_FORMAT@"><![CDATA[(^0\\.[1-3]$|^0\\.[0-2]\\.\\d+$|^0\\.3\\.\\d$|^0\\.3\\.1[0-7]$|^0$)]]></token>\n+ <xml name="usher_download_option">\n+ <when value="download">\n+ <param argument="--use-assignment-cache" type="boolean" truevalue="--use-assignment-cache" falsevalue="" label="Download and use also latest UShER assignment cache?"\n+ help="Get the latest UShER assignment cache from the pangolin-assignment online repository and use it to speed up UShER lineage assignment. Note: Downloading the cached assignments will only pay off for large numbers of input samples." />\n+ </when>\n+ </xml>\n+ <xml name="cached_usher_assignment_cache">\n+ <param name="assignment_cache_release" type="select" optional="true" label="Use corresponding UShER assignment cache?"\n+ help="If the server offers a copy of the UShER assignment cache along with the specified version of pangolin-data, you can select it here to speed up UShER lineage assignment. If no suitable assignment cache is available, it is perfectly fine to proceed without one, and the performance difference will only become obvious with very large numbers of samples.">\n+ <options from_data_table="pangolin_assignment">\n+ <column name="value" index="0" />\n+ <column name="description" index="1" />\n+ <column name="path" index="4" />\n+ <filter type="static_value" column="2" value="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@" />\n+ <filter type="param_value" ref="release" column="0" />\n+ </options>\n+ </param>\n+ </xml>\n+ <xml name="cached_pangolin_data">\n+ <when value="cached">\n+ <param name="release" label="Cached release of pangolin-data" type="select">\n+ <options from_data_table="pangolin_data">\n+ <column name="value" index="0" />\n+ <column name="description" index="1" />\n+ <column name="date" index="3" />\n+ <column name="path" index="4" />\n+ <filter type="sort_by" column="3" />\n+ <filter type="static_value" column="2" value="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@" />\n+ <validator type="no_options" message="No cached constellations release available" />\n+ </options>\n+ </param>\n+ <yield />\n+ </when>\n+ </xml>\n+ <xml name="pangolin_data_sources">\n+ <conditional name="pangolin_data">\n+ <param name="source" type="select" label="Version of pangolin-data to use">\n+ <option value="default">Use pangolin-data version (v@PANGOLIN_DATA_VERSION@) shipped with this version of the tool</option>\n+ <option value="cached">Use specific pangolin-data version cached on this Galaxy server</option>\n+ <option value="download">Download latest available '..b'ckages may be incompatible\n+ with the *pangolin* and *scorpio* version run by the tool, which can\n+ result in failing tool runs, but occasionally also in harder to diagnose\n+ lineage assignment issues.\n \n .. class:: infomark\n \n The exact combination of pangolin, inference engine (UShER/pangoLEARN),\n- scorpio, and data packages used for a particular run of the tool can be\n- extracted from the four "version" columns in the output (see below for\n- details).\n-\n-.. class:: warningmark\n+ scorpio, and data packages that was used for a particular run of the tool\n+ can be extracted from the four "version" columns in the output (see below\n+ for details).\n \n- The "Download latest from web" updates the *pangolin-data* and\n- *constellations* packages but not the software (pangolin and scorpio) using\n- these data packages.\n- If the data package format changes upstream, this can cause the tool run to\n- fail. Cached data packages (or, in the worst case, the built-in data) can\n- serve as a fallback until switching to an updated pangolin tool\n- version.\n-\n+ In addition, lineage assignment with pangolin can be affected by the exact\n+ versions of additional underlying software. The packaged versions of all\n+ relevant dependencies are listed in the *Requirements* section below. This\n+ section is the equivalent to running `pangolin --all-versions` on the\n+ command line except that the listed versions of *pangolin-data* and\n+ *constellations* are the ones installed with pangolin and may have been\n+ overridden with the versions reported in the corresponding output columns\n+ at tool runtime.\n \n **Output**\n \n@@ -317,21 +449,20 @@\n This assignment is sensitive to missing data at key sites.\n \n conflict:\n- In the pangoLEARN model, a given sequence gets assigned to the most likely\n- category based on known diversity.\n If a sequence can fit into more than one category, the conflict score will\n be greater than 0 and reflect the number of categories the sequence could\n fit into.\n- If the conflict score is 0, this means that within the current decision\n- tree there is only one category that the sequence could be assigned to.\n+ If the conflict score is 0, this means that within the current assignment\n+ model / lineage tree there is only one category that the sequence could\n+ plausibly be assigned to.\n \n ambiguity_score:\n This score is a function of the quantity of missing data in a sequence.\n- It represents the proportion of relevant sites in a sequnece which were\n+ It represents the proportion of relevant sites in a sequence which were\n imputed to the reference values.\n A score of 1 indicates that no sites were imputed, while a score of 0\n indicates that more sites were imputed than were not imputed.\n- This score only includes sites which are used by the decision tree to\n+ This score only includes sites which are used by the assignment engine to\n classify a sequence.\n \n scorpio_call:\n@@ -387,7 +518,7 @@\n \n is_designated:\n A boolean (True/False) column indicating whether that particular sequence\n- has been offically designated a lineage.\n+ has been offically designated a lineage (via pango-designation).\n \n qc_status:\n Indicates whether the sequence passed the QC thresholds for minimum length\n@@ -397,11 +528,11 @@\n Notes specific to the QC checks run on the sequences.\n \n note:\n- If any conflicts from the decision tree, this field will output the\n+ If any conflicts arose during assignment, this field will output the\n alternative assignments. If the sequence failed QC this field will describe\n why.\n If the sequence met the SNP thresholds for scorpio to call a constellation,\n- it\xe2\x80\x99ll describe the exact SNP counts of Alt, Ref and Amb (Alternative,\n+ it\xe2\x80\x99ll describe the exact SNP counts of Alt, Ref and Amb (alternative,\n reference and ambiguous) alleles for that call.\n ]]></help>\n <citations>\n' |