| Next changeset 1:4065bcff8e85 (2021-04-27) |
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Commit message:
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse commit f745b23c84a615bf434d717c8c0e553a012f0268 |
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added:
README.rst jbrowse_to_container.py jbrowse_to_container.xml macros.xml |
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| diff -r 000000000000 -r 11033bdad2ca README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Sep 11 05:49:16 2017 -0400 |
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| @@ -0,0 +1,9 @@ +JBrowse to container +==================== + + JBrowse is a fast, embeddable genome browser built completely with + JavaScript and HTML5 + +This tool is only useful when running both JBrowse and Galaxy containers as done +in the +`Galaxy Genome Annotation dockerized GMOD deployment example <https://github.com/galaxy-genome-annotation/dockerized-gmod-deployment>`__ |
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| diff -r 000000000000 -r 11033bdad2ca jbrowse_to_container.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jbrowse_to_container.py Mon Sep 11 05:49:16 2017 -0400 |
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| @@ -0,0 +1,23 @@ +#!/usr/bin/env python +from __future__ import print_function + +import argparse +import base64 + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='Generates an iframe to access a jbrowse instance') + parser.add_argument('external_jbrowse_url', help='Jbrowse full URL') + + args = parser.parse_args() + + # This is base64 encoded to get past the toolshed's filters. + HTML_TPL = """ + PGh0bWw+PGhlYWQ+PHRpdGxlPkVtYmVkZGVkIEpCcm93c2UgQWNjZXNzPC90aXRsZT48c3R5bGUg + dHlwZT0idGV4dC9jc3MiPmJvZHkge3ttYXJnaW46IDA7fX0gaWZyYW1lIHt7Ym9yZGVyOiAwO3dp + ZHRoOiAxMDAlO2hlaWdodDogMTAwJX19PC9zdHlsZT48L2hlYWQ+PGJvZHk+PGlmcmFtZSBzcmM9 + IntiYXNlX3VybH0iPjwvaWZyYW1lPjwvYm9keT48L2h0bWw+DQo= + """ + HTML_TPL = base64.b64decode(HTML_TPL.replace('\n', '')) + +print(HTML_TPL.format(base_url=args.external_jbrowse_url)) |
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| diff -r 000000000000 -r 11033bdad2ca jbrowse_to_container.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jbrowse_to_container.xml Mon Sep 11 05:49:16 2017 -0400 |
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| @@ -0,0 +1,80 @@ +<?xml version="1.0"?> +<tool id="jbrowse_to_container" name="Add organisms to JBrowse container" version="@WRAPPER_VERSION@"> + <description>will replace any existing organism</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ + + if [ -z "@DATA_DIR@" ]; then + echo '@DATA_DIR@ variable must be set to use this tool'; + exit 1; + fi; + + rm -rf "@DATA_DIR@/"* + + && + + #for $org in $organisms: + #if $org.advanced.unique_id: + #set dataset_name = $org.advanced.unique_id + #else: + #set dataset_name = $org.jbrowse.id + #end if + + cp -R '${org.jbrowse.extra_files_path}/data/' "@DATA_DIR@/${dataset_name}" + + && + + echo -e "[general]\ndataset_id = ${dataset_name}" >> "@DATA_DIR@/${dataset_name}/tracks.conf" + + && + #end for + + cp $trackList "@DATA_DIR@/datasets.conf" + + && + + python $__tool_directory__/jbrowse_to_container.py @JBROWSE_BASE_URL@ > $output + ]]></command> + <configfiles> + <configfile name="trackList"> + <![CDATA[ +#for $org in $organisms: +#if $org.advanced.unique_id: +#set dataset_name = $org.advanced.unique_id +#else: +#set dataset_name = $org.jbrowse.id +#end if +[datasets.$dataset_name] +url = ?data=data/${dataset_name} +name = $org.name +#end for + ]]> + </configfile> + </configfiles> + <inputs> + <repeat name="organisms" title="Organism"> + <param name="jbrowse" type="data" format="html" label="JBrowse HTML Output" /> + <param name="name" type="text" label="Display name" optional="False" /> + <section name="advanced" title="Advanced" expanded="False"> + <param name="unique_id" type="text" label="Unique ID" help="will be used in HTTP links (default=auto generated id). WARNING: If set, pay attention to have different ID for each dataset." optional="True"> + <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator> + </param> + </section> + </repeat> + </inputs> + <outputs> + <data format="html" name="output"/> + </outputs> + <help><![CDATA[ +**What it does** +Adds an organism to a JBrowse instance. The tool takes the output of a +JBrowse run as that contains all of the necessary information for which +tracks are appropriate for a given analysis. + +@ATTRIBUTION@ + ]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r 11033bdad2ca macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Sep 11 05:49:16 2017 -0400 |
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| @@ -0,0 +1,35 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.7">python</requirement> + <yield/> + </requirements> + </xml> + + <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> + <token name="@JBROWSE_BASE_URL@">\$GALAXY_JBROWSE_SHARED_URL</token> + <token name="@WRAPPER_VERSION@">0.5.1</token> + + <xml name="stdio"> + <stdio> + <exit_code range="1:"/> + <exit_code range=":-1"/> + <regex match="Error:"/> + <regex match="Exception:"/> + </stdio> + </xml> + + <token name="@ATTRIBUTION@"><![CDATA[ +**Attribution** + +This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by Eric Rasche +]]> + </token> + + <xml name="citations"> + <citations> + <citation type="doi">10.1101/gr.094607.109</citation> + </citations> + </xml> +</macros> |