Mercurial > repos > iuc > crossmap_bed

changeset 2:79f9e32b380b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
author iuc
date Fri, 20 Oct 2017 02:48:24 -0400
parents 1e881a00d8ff
children b49e453e6f97
files crossmap_bed.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, 643 insertions(+), 91 deletions(-) [+]
line wrap: on
line diff
--- a/crossmap_bed.xml	Tue Sep 26 06:05:09 2017 -0400
+++ b/crossmap_bed.xml	Fri Oct 20 02:48:24 2017 -0400
@@ -7,84 +7,96 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
 
-    <command><![CDATA[
-        #set $input_file = str($seq_source.input)
-
-        CrossMap.py bed
-            '${chain_source.input_chain}'
+<!--
+1. CrossMap bed x.chain in.bed > out.bed
+stdout/out.bed: valid and invalid combined
 
-            '${input_file}'
+2. CrossMap bed x.chain in.bed out.bed
+out.bed: valid only
+out.bed.unmap: invalid only
+-->
+    <command><![CDATA[
+CrossMap.py bed
+'${chain_source.input_chain}'
 
-            #if str($include_fails) == "True"
-            >
-            #end if
+'${input}'
 
-            '${output}'
+#if $merge_unmapped_entries:
+    > '${output_combined}'
+#else:
+    '${output_valid}'
+    && mv '${output_valid}.unmap' '${output_failed}'
+#end if
+
     ]]></command>
 
 
     <inputs>
-       <conditional name="seq_source">
-            <expand macro="source" />
+        <param name="input" type="data" format="bed" label="BED file"
+               help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>
 
-            <when value="cached">
-                <param format="bed" name="input" type="data" label="BED file"
-                       help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.">
-                    <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="bed" name="input" label="BED file"
-                       help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns."/>
-            </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="merge_unmapped_entries" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Merge failed and converted entries into single file"/>
     </inputs>
 
     <outputs>
-        <data format="bed" name="output" label="${tool.name} on ${on_string}" />
-        <data format="text" name="output2" label="${tool.name} (bedgraph) on ${on_string}" />
+        <data name="output_valid" format="bed" label="${tool.name} (valid only) on ${on_string}">
+            <filter>merge_unmapped_entries is False</filter>
+        </data>
+        <data name="output_failed" format="bed" label="${tool.name} (failed only) on ${on_string}">
+            <filter>merge_unmapped_entries is False</filter>
+        </data>
+
+        <data name="output_combined" format="bed" label="${tool.name} on ${on_string}">
+            <filter>merge_unmapped_entries is True</filter>
+        </data>
     </outputs>
 
     <tests>
-    <!-- BED -->
-        <test>
+        <test><!-- this test only contains perfect entries that do get liftOvered (separate output) -->
+            <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
             <param name="index_source" value="history"/>
-            <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
             <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
-            <param name="include_fails" value="False"/>
+            <param name="merge_unmapped_entries" value="false" />
 
-            <output name="output" file="test_bed_01_output_a__only-matches.bed"/>
+            <output name="output_valid" file="test_bed_01_output_a__only-matches.bed"/>
+            <output name="output_failed" file="test_bed_01_output_a__only_fails.bed"/>
         </test>
-        <test>
+        <test><!-- this test only contains perfect entries that do get liftOvered (merged output) -->
+            <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
             <param name="index_source" value="history"/>
-            <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
             <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
-            <param name="include_fails" value="True"/>
+            <param name="merge_unmapped_entries" value="true" />
+
+            <output name="output_combined" file="test_bed_01_output_a__all.bed"/>
+        </test>
 
-            <output name="output" file="test_bed_01_output_a__all.bed"/>
-        </test>
-        <test>
+        <test><!-- this test only contains imperfect entries that do get liftOvered (separate output) -->
+            <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
             <param name="index_source" value="history"/>
-            <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
             <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
-            <param name="include_fails" value="False"/>
+            <param name="merge_unmapped_entries" value="false" />
 
-            <output name="output" file="test_bed_02_output_a__only-matches.bed"/>
+            <output name="output_valid" file="test_bed_02_output_a__only-matches.bed"/>
+            <output name="output_failed" file="test_bed_02_output_a__only_fails.bed"/>
         </test>
-        <test>
-            <param name="index_source" value="history"/>
+        <test><!-- this test only contains imperfect entries that do get liftOvered (separate output) -->
             <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
+            <param name="index_source" value="history"/>
             <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
-            <param name="include_fails" value="True"/>
+            <param name="merge_unmapped_entries" value="true" />
+
+            <output name="output_combined" file="test_bed_02_output_a__all.bed"/>
+        </test>
 
-            <output name="output" file="test_bed_02_output_a__all.bed"/>
+        <test><!-- clone of first test: tests cached reference chain file -->
+            <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
+            <param name="index_source" value="cached"/>
+            <param name="merge_unmapped_entries" value="false" />
+
+            <output name="output_valid" file="test_bed_01_output_a__only-matches.bed"/>
+            <output name="output_failed" file="test_bed_01_output_a__only_fails.bed"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -96,36 +108,35 @@
 BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.
 BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
 
-    A BED (Browser Extensible Data) file is a tab-delimited text file
-    describing genome regions or gene annotations. It is the standard file
-    format used by UCSC. It consists of one line per feature, each containing
-    3-12 columns. CrossMap converts BED files with less than 12 columns to a
-    different assembly by updating the chromosome and genome coordinates only;
-    all other columns remain unchanged. Regions from old assembly mapping to
-    multiple locations to the new assembly will be split. For 12-columns BED
-    files, all columns will be updated accordingly except the 4th column (name
-    of bed line), 5th column (score value) and 9th column (RGB value describing
-    the display color). 12-column BED files usually define multiple blocks (eg.
-    exon); if any of the exons fails to map to a new assembly, the whole BED
-    line is skipped.
+A BED (Browser Extensible Data) file is a tab-delimited text file
+describing genome regions or gene annotations. It is the standard file
+format used by UCSC. It consists of one line per feature, each containing
+3-12 columns. CrossMap converts BED files with less than 12 columns to a
+different assembly by updating the chromosome and genome coordinates only;
+all other columns remain unchanged. Regions from old assembly mapping to
+multiple locations to the new assembly will be split. For 12-columns BED
+files, all columns will be updated accordingly except the 4th column (name
+of bed line), 5th column (score value) and 9th column (RGB value describing
+the display color). 12-column BED files usually define multiple blocks (eg.
+exon); if any of the exons fails to map to a new assembly, the whole BED
+line is skipped.
 
-    NOTE:
+Notes:
 
-    1. For BED-like formats mentioned above, CrossMap only updates “chrom (1st
-       column)”, “start (2nd column) ”, “end (3rd column) ” and “strand” (if
-       any). All other columns will keep AS-IS.
-    2. Lines starting with ‘#’, ‘browser’, ‘track’ will be skipped.
-    3. Lines will less than 3 columns will be skipped.
-    4. 2nd-column and 3-column must be integer, otherwise skipped.
-    5. “+” strand is assumed if no strand information was found.
-    6. For standard BED format (12 columns). If any of the defined exon blocks
-       cannot be uniquely mapped to target assembly, the whole entry will be
-       skipped.
-    7. If input region cannot be consecutively mapped target assembly, it will be split.
-    8. *.unmap file contains regions that cannot be unambiguously converted.
+1. For BED-like formats mentioned above, CrossMap only updates “chrom (1st
+   column)”, “start (2nd column) ”, “end (3rd column) ” and “strand” (if
+   any). All other columns will keep AS-IS.
+2. Lines starting with ‘#’, ‘browser’, ‘track’ will be skipped.
+3. Lines will less than 3 columns will be skipped.
+4. 2nd-column and 3-column must be integer, otherwise skipped.
+5. “+” strand is assumed if no strand information was found.
+6. For standard BED format (12 columns). If any of the defined exon blocks
+   cannot be uniquely mapped to target assembly, the whole entry will be
+   skipped.
+7. If input region cannot be consecutively mapped target assembly, it will be split.
+8. \*.unmap file contains regions that cannot be unambiguously converted.
 
-Please see `the manual <http://crossmap.sourceforge.net/#convert-bed-format-files>`__ for more details.
-]]></help>
+    ]]></help>
 
     <citations>
         <citation type="doi">10.1093/bioinformatics/btt730</citation>
--- a/macros.xml	Tue Sep 26 06:05:09 2017 -0400
+++ b/macros.xml	Fri Oct 20 02:48:24 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">
@@ -26,25 +27,18 @@
             </param>
             <when value="cached">
                 <param name="input_chain" type="select" label="Lift Over To">
-                    <options from_file="liftOver.loc">
-                        <column name="dbkey" index="0"/><!-- species/build 'from' -->
-                        <column name="name" index="1"/><!-- species/build 'to' -->
-                        <column name="value" index="2"/><!-- path of chain file -->
-                        <filter type="data_meta" ref="input" key="dbkey"/>
+                    <options from_data_table="liftOver">
+                        <!--
+                        <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 02:48:24 2017 -0400
@@ -0,0 +1,498 @@
+chain 21270171362 chr1 249250621 + 10000 249233096 chr1 247249719 + 0 247199719 2
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+5088	1	0
+2185	10046	10048
+949	4	4
+35	1	1
+2874	0	1
+6717	0	1
+2823	1	0
+703	0	4
+5143	1	0
+2490	10	10
+162	7	7
+6308	0	15
+15177535	152352	260003
+2532	1	0
+1633	2	2
+24207544	3000000	4400000
+60453436	0	4
+40076813	20999	20000
+8195	1	1
+44	1	1
+1408	1	1
+33	1	1
+172	3	4
+25	1	1
+538	13	13
+173	1	1
+27	1	1
+636	1	1
+28	1	1
+470	3	3
+112	1	1
+375	1	1
+26	26	0
+115	78	0
+52	23	0
+104	26	0
+15	231	0
+56	1	1
+20	1	1
+815	16	16
+484	1	1
+49	18	0
+509	4	3
+23	1	1
+391	1	1
+44	1	1
+1278	0	4
+32	1	1
+263	4	0
+27	1	1
+2416	0	2
+3184	43	43
+1150	13	13
+736	1	1
+47	1	1
+1416	1	1
+20	1	1
+1020	1	1
+25	1	1
+482	5	0
+716	1	0
+1697	1	1
+29	1	1
+1270261	23108	27000
+40930	1	0
+17455	1	1
+28	4	4
+43	0	491
+1679	1	1
+33	7	5
+29	1	3
+54863	53	16
+7653	2	2
+29	2	2
+15	0	30
+180	0	75
+215	45	0
+360	915	0
+6188	96	0
+17	288	0
+1388	1	1
+37	1	1
+7956	0	1
+374	0	1
+2442058
+
+chain 310844 chr4 191154276 + 9241835 9252105 chr4 191273063 + 8941714 8947231 850
+2726	14	14
+243	9	9
+78	4	4
+157	213	211
+265	85	85
+524	4751	0
+379	283	283
+539
+
+chain 9105 chr4 191154276 + 8982741 8983189 chr10 135374737 - 120304868 120305301 22041837
+59	380	365
+9
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/liftOver.loc	Fri Oct 20 02:48:24 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	${__HERE__}/aToB.over.chain
Binary file test-data/test_bam_01_output_a.bam has changed
Binary file test-data/test_bam_01_output_a.unmap.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_bed_02_output_a__only_fails.bed	Fri Oct 20 02:48:24 2017 -0400
@@ -0,0 +1,5 @@
+chr1	100	10000
+chr2	100	10000
+chr3	100	10000
+chr4	8941700 8947200
+chr5	1	100000000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Fri Oct 20 02:48:24 2017 -0400
@@ -0,0 +1,12 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__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>