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Make tool version explicit (Job runner would assume 1.0.0)

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peterjc
2015-03-09 15:21:48 +00:00
parent 05e65b9f2d
commit fce2184e5b
61 changed files with 62 additions and 62 deletions
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tools/data_source/access_libraries.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool name="Access Libraries" id="library_access1">
<tool name="Access Libraries" id="library_access1" version="1.0.0">
<description>stored locally</description>
<inputs action="/library/index" method="get" target="_parent">
<param name="default_action" type="hidden" value="import_to_histories" />
tools/data_source/bed_convert.xml
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@@ -1,4 +1,4 @@
<tool id="BED File Converter1" name="BED File Converter">
<tool id="BED File Converter1" name="BED File Converter" version="1.0.0">
<description>creates a bed or xbed file containing from text query</description>
<command>noop</command>
<inputs>
tools/data_source/echo.xml
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@@ -1,6 +1,6 @@
<?xml version="1.0"?>
<tool name="Echo" id="echo1">
<tool name="Echo" id="echo1" version="1.0.0">
<description>
echoes parameters
tools/data_source/eupathdb.xml
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@@ -1,4 +1,4 @@
<tool name="EuPathDB" id="eupathdb" tool_type="data_source" url_method="post">
<tool name="EuPathDB" id="eupathdb" tool_type="data_source" url_method="post" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://eupathdb.org/eupathdb/queries_tools.jsp" check_values="false" method="get">
tools/data_source/fly_modencode.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool name="modENCODE fly" id="modENCODEfly" tool_type="data_source">
<tool name="modENCODE fly" id="modENCODEfly" tool_type="data_source" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://modencode.oicr.on.ca/fgb2/gbrowse/fly" check_values="false" target="_top">
tools/data_source/flymine.xml
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@@ -4,7 +4,7 @@
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
-->
<tool name="Flymine" id="flymine" tool_type="data_source">
<tool name="Flymine" id="flymine" tool_type="data_source" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://www.flymine.org" check_values="false" method="get">
tools/data_source/flymine_test.xml
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@@ -4,7 +4,7 @@
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
-->
<tool name="Flymine test" id="flymine_test" tool_type="data_source">
<tool name="Flymine test" id="flymine_test" tool_type="data_source" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://preview.flymine.org/preview/begin.do" check_values="false" method="get">
tools/data_source/genbank.xml
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@@ -1,4 +1,4 @@
<tool id="genbank" name="Connect to Genbank">
<tool id="genbank" name="Connect to Genbank" version="1.0.0">
<!-- <description>queries genbank</description> -->
<command interpreter="python">genbank.py $mode "$text" $output</command>
<inputs>
tools/data_source/import.xml
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@@ -1,4 +1,4 @@
<tool id="Featured datasets4" name="Featured datasets">
<tool id="Featured datasets4" name="Featured datasets" version="1.0.0">
<description>(PSU prepared queries)</description>
<command interpreter="python">import.py $data $output</command>
<inputs>
tools/data_source/metabolicmine.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool name="metabolicMine" id="metabolicmine" tool_type="data_source">
<tool name="metabolicMine" id="metabolicmine" tool_type="data_source" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://www.metabolicmine.org/beta/begin.do" check_values="false" method="get">
tools/data_source/microbial_import.xml
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@@ -1,4 +1,4 @@
<tool id="microbial_import1" name="Get Microbial Data">
<tool id="microbial_import1" name="Get Microbial Data" version="1.0.0">
<command interpreter="python">microbial_import.py $CDS,$tRNA,$rRNA,$sequence,$GeneMark,$GeneMarkHMM,$Glimmer3 $output ${GALAXY_DATA_INDEX_DIR}/microbial_data.loc</command>
<inputs>
<param name="kingdom" type="select" label="Select the Desired Kingdom">
tools/data_source/modmine.xml
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@@ -4,7 +4,7 @@
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
-->
<tool name="modENCODE modMine" id="modmine" tool_type="data_source">
<tool name="modENCODE modMine" id="modmine" tool_type="data_source" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://intermine.modencode.org/" check_values="false" method="get">
tools/data_source/mousemine.xml
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@@ -4,7 +4,7 @@
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
-->
<tool name="MouseMine" id="mousemine" tool_type="data_source">
<tool name="MouseMine" id="mousemine" tool_type="data_source" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://www.mousemine.org/mousemine/begin.do" check_values="false" method="get">
tools/data_source/ratmine.xml
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@@ -4,7 +4,7 @@
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
-->
<tool name="Ratmine" id="ratmine" tool_type="data_source">
<tool name="Ratmine" id="ratmine" tool_type="data_source" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://ratmine.mcw.edu/ratmine/begin.do" check_values="false" method="get">
tools/data_source/ucsc_archaea.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool name="UCSC Archaea" id="ucsc_proxy">
<tool name="UCSC Archaea" id="ucsc_proxy" version="1.0.0">
<description>table browser</description>
tools/data_source/ucsc_proxy.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool name="UCSC Main" id="ucsc_proxy">
<tool name="UCSC Main" id="ucsc_proxy" version="1.0.0">
<description>table browser proxy</description>
tools/data_source/ucsc_tablebrowser.xml
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@@ -4,7 +4,7 @@
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
-->
<tool name="UCSC Main" id="ucsc_table_direct1" tool_type="data_source">
<tool name="UCSC Main" id="ucsc_table_direct1" tool_type="data_source" version="1.0.0">
<description>table browser</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="https://genome.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
tools/data_source/ucsc_tablebrowser_archaea.xml
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@@ -4,7 +4,7 @@
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
-->
<tool name="UCSC Archaea" id="ucsc_table_direct_archaea1" tool_type="data_source">
<tool name="UCSC Archaea" id="ucsc_table_direct_archaea1" tool_type="data_source" version="1.0.0">
<description>table browser</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://archaea.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
tools/data_source/ucsc_tablebrowser_test.xml
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@@ -4,7 +4,7 @@
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
-->
<tool name="UCSC Test" id="ucsc_table_direct_test1" tool_type="data_source">
<tool name="UCSC Test" id="ucsc_table_direct_test1" tool_type="data_source" version="1.0.0">
<description>table browser</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://genome-test.cse.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
tools/data_source/ucsc_testproxy.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool name="UCSC Test" id="ucsc_testproxy">
<tool name="UCSC Test" id="ucsc_testproxy" version="1.0.0">
<description>table browser proxy</description>
tools/data_source/worm_modencode.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool name="modENCODE worm" id="modENCODEworm" tool_type="data_source">
<tool name="modENCODE worm" id="modENCODEworm" tool_type="data_source" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://modencode.oicr.on.ca/fgb2/gbrowse/worm" check_values="false" target="_top">
tools/data_source/wormbase_test.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool name="Wormbase" id="wormbase_test" tool_type="data_source">
<tool name="Wormbase" id="wormbase_test" tool_type="data_source" version="1.0.0">
<description>test server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://dev.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" target="_top">
tools/data_source/yeastmine.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool name="YeastMine" id="yeastmine" tool_type="data_source">
<tool name="YeastMine" id="yeastmine" tool_type="data_source" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://yeastmine.yeastgenome.org/yeastmine/begin.do" check_values="false" method="get">
tools/data_source/zebrafishmine.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool name="ZebrafishMine" id="zebrafishmine" tool_type="data_source">
<tool name="ZebrafishMine" id="zebrafishmine" tool_type="data_source" version="1.0.0">
<description>server</description>
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://zebrafishmine.org/begin.do" check_values="false" method="get">