changeset 7:1b57bf1bb4ec draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
author iuc
date Fri, 20 Oct 2017 02:48:09 -0400
parents 9ca13f08f2f7
children 45c57bf42470
files crossmap_gff.xml macros.xml test-data/cached_locally/aToB.over.chain test-data/cached_locally/liftOver.loc test-data/test_bam_01_output_a.bam test-data/test_bam_01_output_a.unmap.bam test-data/test_bed_01_output_a__only_fails.bed test-data/test_bed_02_output_a__only_fails.bed tool_data_table_conf.xml.test
diffstat 8 files changed, 583 insertions(+), 53 deletions(-) [+]
line wrap: on
line diff
--- a/crossmap_gff.xml	Tue Sep 26 06:09:26 2017 -0400
+++ b/crossmap_gff.xml	Fri Oct 20 02:48:09 2017 -0400
@@ -8,59 +8,49 @@
     <expand macro="version_command"/>
 
     <command><![CDATA[
-        CrossMap.py gff
-            '${chain_source.input_chain}'
-            '${seq_source.input}'
+CrossMap.py gff
+'${chain_source.input_chain}'
+'${input}'
 
-            #if str($include_fails) == "True"
-            >
-            #end if
+#if str($include_fails) == "True"
+    >
+#end if
 
-            '${output}'
+'${output}'
     ]]></command>
 
     <inputs>
-        <conditional name="seq_source">
-            <expand macro="source" />
+        <param name="input" type="data" format="gtf,gff,gff3" label="GTF/GFF file"/>
 
-            <when value="cached">
-                <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file">
-                    <validator type="unspecified_build"/>
-                    <!-- Gives error in tests
-                    <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build."/>
-                    -->
-                </param>
-            </when>
-            <when value="history">
-                <param type="data" format="gtf,gff,gff3" name="input"       label="GTF/GFF file"/>
-            </when>
-        </conditional>
         <expand macro="chain" />
 
-        <param name="include_fails" type="boolean" truevalue="True" checked="false" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')"/>
+        <param name="include_fails" type="boolean" truevalue="True" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')"/>
     </inputs>
 
     <outputs>
-        <!-- GTF/GFF3? test... -->
-        <data format="gff" name="output" label="${tool.name} on ${on_string}" />
+        <data name="output" format="gff" label="${tool.name} on ${on_string}" />
     </outputs>
 
     <tests>
-    <!-- GFF -->
         <test>
-            <param name="input_format" value="gff"/>
+            <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
             <param name="index_source" value="history"/>
-            <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
             <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
             <param name="include_fails" value="False"/>
 
             <output name="output" file="test_gff_01_output_a__only-matches.gtf"/>
         </test>
         <test>
-            <param name="input_format" value="gff"/>
+            <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
             <param name="index_source" value="history"/>
+            <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
+            <param name="include_fails" value="True"/>
+
+            <output name="output" file="test_gff_01_output_a__all.gtf"/>
+        </test>
+        <test><!-- cached chain file -->
             <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
-            <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
+            <param name="index_source" value="cached"/>
             <param name="include_fails" value="True"/>
 
             <output name="output" file="test_gff_01_output_a__all.gtf"/>
@@ -73,20 +63,19 @@
 ---------
 Your input data should be either GTF/GFF2.5 or GFF3 format.
 
-    GFF (General Feature Format) is another plain text file used to describe
-    gene structure. GTF (Gene Transfer Format) is a refined version of GTF. The
-    first eight fields are the same as GFF. Only chromosome and genome
-    coordinates are updated. The format of output is determined from the input.
+GFF (General Feature Format) is another plain text file used to describe
+gene structure. GTF (Gene Transfer Format) is a refined version of GTF. The
+first eight fields are the same as GFF. Only chromosome and genome
+coordinates are updated. The format of output is determined from the input.
 
-    NOTE:
+Notes:
 
-    - Each feature (exon, intron, UTR, etc) is processed separately and
-      independently, and we do NOT check if features originally belonging to
-      the same gene were converted into the same gene.
-    - If user want to liftover gene annotation files, use BED12 format.
+- Each feature (exon, intron, UTR, etc) is processed separately and
+  independently, and we do NOT check if features originally belonging to
+  the same gene were converted into the same gene.
+- If user want to liftover gene annotation files, use BED12 format.
 
-Please see `the manual <http://crossmap.sourceforge.net/#convert-gff-gtf-format-files>`__ for more details
-]]></help>
+    ]]></help>
 
     <citations>
         <citation type="doi">10.1093/bioinformatics/btt730</citation>
--- a/macros.xml	Tue Sep 26 06:09:26 2017 -0400
+++ b/macros.xml	Fri Oct 20 02:48:09 2017 -0400
@@ -2,12 +2,11 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="324">ucsc-wigtobigwig</requirement>
-            <requirement type="package" version="0.2.2">crossmap</requirement>
+            <requirement type="package" version="0.2.5">crossmap</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@WRAPPER_VERSION@">0.2.2</token>
+    <token name="@WRAPPER_VERSION@">0.2.5</token>
     <xml name="stdio">
         <stdio>
             <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>
@@ -16,7 +15,9 @@
         </stdio>
     </xml>
     <xml name="version_command">
-        <version_command>CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command>
+        <version_command><![CDATA[
+CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'
+        ]]></version_command>
     </xml>
     <xml name="chain">
         <conditional name="chain_source">
@@ -28,23 +29,16 @@
                 <param name="input_chain" type="select" label="Lift Over To">
                     <options from_data_table="liftOver">
                         <!--
-                        planemo can't update this ?
-                            <filter type="data_meta" ref="input" key="dbkey"/>
+                        <filter type="data_meta" ref="input" key="dbkey" column="0"/>
                         -->
                     </options>
                 </param>
             </when>
             <when value="history">
-                <param type="data" format="csv" name="input_chain" label="LiftOver chain file"/>
+                <param name="input_chain" type="data" format="csv" label="LiftOver chain file"/>
             </when>
         </conditional>
     </xml>
-    <xml name="source">
-        <param name="index_source" type="select" label="Source for Input Data">
-            <option value="cached">Local data (in galaxy)</option>
-            <option value="history">From History</option>
-        </param>
-    </xml>
     <token name="@HELP_GENERAL@">
 CrossMap
 --------
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/aToB.over.chain	Fri Oct 20 02:48:09 2017 -0400
@@ -0,0 +1,498 @@
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+
+chain 22466185064 chr2 243199373 + 10000 243102476 chr2 242951149 + 0 242751149 1
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+
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+
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+
+chain 9105 chr4 191154276 + 8982741 8983189 chr10 135374737 - 120304868 120305301 22041837
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+9
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/liftOver.loc	Fri Oct 20 02:48:09 2017 -0400
@@ -0,0 +1,32 @@
+#This is a sample file distributed with Galaxy that is used by the
+#liftOver tools.  The liftOver.loc file has this format (white space 
+#characters are TAB characters):
+#
+#<FromSpecies>	<ToSpecies>	<PathToChainFile>
+#
+#So, for example, if you had the chain file to convert from anoCar1 to galGal3
+#located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, 
+#then the liftOver.loc entry would look like this:
+#
+#<FromSpecies>  <ToSpecies> <PathToChainFile>
+#<dbkey>        <name>      <value>
+#
+#anoCar1	galGal3		/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
+#
+#and your /depot/data2/galaxy/anoCar1/liftOver directory would 
+#contain all of your "chain" files (e.g.):
+#
+#-rw-rw-r-- 1 gua110 galaxy 24046079 2008-01-16 14:20 anoCar1ToGalGal3.over.chain
+#-rw-rw-r-- 1 gua110 galaxy 13216668 2008-01-16 14:20 anoCar1ToGasAcu1.over.chain
+#-rw-rw-r-- 1 gua110 galaxy 29597067 2008-01-16 14:20 anoCar1ToHg18.over.chain
+#...etc...
+#
+#Your liftOver.loc file should include an entry per line for each build you can
+#convert.  For example:
+#
+#anoCar1	galGal3	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
+#anoCar1	gasAcu1	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain
+#anoCar1	hg18	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain
+#...etc...
+
+A	B	${__HERE__}/aToB.over.chain
Binary file test-data/test_bam_01_output_a.bam has changed
Binary file test-data/test_bam_01_output_a.unmap.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_bed_02_output_a__only_fails.bed	Fri Oct 20 02:48:09 2017 -0400
@@ -0,0 +1,5 @@
+chr1	100	10000
+chr2	100	10000
+chr3	100	10000
+chr4	8941700 8947200
+chr5	1	100000000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Fri Oct 20 02:48:09 2017 -0400
@@ -0,0 +1,12 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/cached_locally/all_fasta.loc" />
+    </table>
+    <!-- Locations of all liftOver files -->
+    <table name="liftOver" comment_char="#">
+        <columns>dbkey, name, value</columns>
+        <file path="${__HERE__}/test-data/cached_locally/liftOver.loc" />
+    </table>
+</tables>