Mercurial > repos > iuc > gffcompare

changeset 1:c80cdc2eac6d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
author iuc
date Wed, 12 Dec 2018 03:19:14 -0500
parents 3c97c841a443
children f99d7825a501
files gffcompare.xml test-data/gffcompare_out1-1.refmap test-data/gffcompare_out1-1.tmap test-data/gffcompare_out1-2.refmap test-data/gffcompare_out1-2.tmap
diffstat 5 files changed, 185 insertions(+), 43 deletions(-) [+]
line wrap: on
line diff
--- a/gffcompare.xml	Fri Apr 07 16:02:07 2017 -0400
+++ b/gffcompare.xml	Wed Dec 12 03:19:14 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="gffcompare" name="GffCompare" version="0.9.8">
+<tool id="gffcompare" name="GffCompare" version="0.9.8+galaxy1">
     <description>compare assembled transcripts to a reference annotation</description>
     <requirements>
         <requirement type="package" version="0.9.8">gffcompare</requirement>
@@ -10,35 +10,47 @@
         <regex match="Exception" />
     </stdio>
     <version_command>gffcompare -v | awk '{print $2}'</version_command>
-    <command>
-        <![CDATA[
-            #set $input_gtf = "' '".join(str($inputs).split(','))
-            #if $seq_data.use_seq_data == "Yes":
-                #if $seq_data.seq_source.index_source == "history":
-                    ln -s '$seq_data.seq_source.ref_file' ref_seq.fa &&
-                #else:
-                    ln -s '${seq_data.seq_source.index.fields.path}' ref_seq.fa &&
-                #end if
-            #end if
-            gffcompare
-            ## Use annotation reference?
-            #if $annotation.use_ref_annotation == "Yes":
-                -r '$annotation.reference_annotation' $annotation.ignore_nonoverlapping_reference $annotation.ignore_nonoverlapping_transfrags
-            #end if
+    <command><![CDATA[
+#import re
+#set escaped_element_identifiers = [re.sub('[^\w\-]', '_', str(_.element_identifier)) for _ in $gffinputs]
+#for $input, $escaped_element_identifier in zip($gffinputs, $escaped_element_identifiers):
+    ln -s '$input' '$escaped_element_identifier' &&
+#end for
+#if $seq_data.use_seq_data == "Yes":
+    #if $seq_data.seq_source.index_source == "history":
+        ln -s '$seq_data.seq_source.ref_file' ref_seq.fa &&
+    #else:
+        ln -s '${seq_data.seq_source.index.fields.path}' ref_seq.fa &&
+    #end if
+#end if
 
-            ## Use sequence data?
-
-            #if $seq_data.use_seq_data == "Yes":
-                -s ref_seq.fa
-            #end if
+gffcompare
+## Use annotation reference?
+#if $annotation.use_ref_annotation == "Yes":
+    -r '$annotation.reference_annotation'
+    $annotation.ignore_nonoverlapping_reference
+    $annotation.ignore_nonoverlapping_transfrags
+    #if not $annotation.refmap_tmap:
+        -T
+    #end if
+#end if
 
-            $discard_single_exon -e $max_dist_exon -d $max_dist_group $discard_intron_redundant_transfrags
+## Use sequence data?
+#if $seq_data.use_seq_data == "Yes":
+    -s ref_seq.fa
+#end if
 
-            '$input_gtf'
-        ]]>
-    </command>
+$discard_single_exon
+-e $max_dist_exon
+-d $max_dist_group
+$discard_intron_redundant_transfrags
+
+#for $escaped_element_identifier in $escaped_element_identifiers:
+    '$escaped_element_identifier'
+#end for
+    ]]></command>
     <inputs>
-        <param format="gtf" name="inputs" type="data" label="GTF inputs for comparison" help="" multiple="true" />
+        <param format="gtf" name="gffinputs" type="data" label="GTF inputs for comparison" help="" multiple="true" />
         <conditional name="annotation">
             <param label="Use Reference Annotation" name="use_ref_annotation" type="select">
                 <option value="No">No</option>
@@ -48,6 +60,10 @@
                 <param argument="-r" format="gff3,gtf" help="Requires an annotation file in GFF3 or GTF format." label="Reference Annotation" name="reference_annotation" type="data" />
                 <param argument="-R" falsevalue="" help="consider only the reference transcripts that overlap any of the input transfrags (Sn correction)" label="Ignore reference transcripts that are not overlapped by any input transfrags" name="ignore_nonoverlapping_reference" truevalue="-R" type="boolean" />
                 <param argument="-Q" falsevalue="" help="consider only the input transcripts that overlap any of the reference transcripts (Sp correction). Warning: this will discard all 'novel' loci!" label="Ignore input transcripts that are not overlapped by any reference transcripts" name="ignore_nonoverlapping_transfrags" truevalue="-Q" type="boolean" />
+                <param argument="-T" name="refmap_tmap" label="Generate tmap and refmap files for each input file" type="select" multiple="True">
+                    <option value="refmap" selected="True">refmap</option>
+                    <option value="tmap" selected="True">tmap</option>
+                </param>
             </when>
             <when value="No">
             </when>
@@ -57,7 +73,7 @@
                 <option value="Yes">Yes</option>
                 <option value="No">No</option>
             </param>
-            <when value="No" />
+            <when value="No"/>
             <when value="Yes">
                 <conditional name="seq_source">
                     <param label="Choose the source for the reference list" name="index_source" type="select">
@@ -67,7 +83,7 @@
                     <when value="cached">
                         <param argument="-s" label="Using reference genome" name="index" type="select">
                             <options from_data_table="fasta_indexes">
-                                <filter column="1" key="dbkey" ref="inputs" type="data_meta" />
+                                <filter column="1" key="dbkey" ref="gffinputs" type="data_meta" />
                                 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
                             </options>
                         </param>
@@ -90,44 +106,65 @@
     <outputs>
         <data format="txt" from_work_dir="gffcmp.stats" label="${tool.name} on ${on_string}: transcript accuracy" name="transcripts_stats" />
         <data format="tabular" from_work_dir="gffcmp.loci" label="${tool.name} on ${on_string}: loci" name="transcripts_loci" />
-        <data format="tabular" from_work_dir="gffcmp.tracking" label="${tool.name} on ${on_string}: data ${inputs[0].hid} tracking file" name="transcripts_tracking" />
+        <data format="tabular" from_work_dir="gffcmp.tracking" label="${tool.name} on ${on_string}: data ${gffinputs[0].hid} tracking file" name="transcripts_tracking" />
         <data format="gtf" from_work_dir="gffcmp.combined.gtf" label="${tool.name} on ${on_string}: combined transcripts" name="transcripts_combined">
-            <filter>(use_seq_data == 'No')</filter>
+            <filter>isinstance(gffinputs, list)</filter>
         </data>
         <data format="gtf" from_work_dir="gffcmp.annotated.gtf" label="${tool.name} on ${on_string}: annotated transcripts" name="transcripts_annotated">
-            <filter>(use_seq_data == 'Yes')</filter>
+            <filter>not isinstance(gffinputs, list)</filter>
         </data>
+        <collection name="refmap_output" type="list" label="${tool.name} on ${on_string}: refmap">
+            <discover_datasets pattern="gffcmp\.(?P&lt;designation&gt;.+)\.refmap" ext="tabular" />
+            <filter>annotation['use_ref_annotation'] == 'Yes' and annotation['refmap_tmap'] != None and 'refmap' in annotation['refmap_tmap']</filter>
+        </collection>
+        <collection name="tmap_output" type="list" label="${tool.name} on ${on_string}: tmap">
+            <discover_datasets pattern="gffcmp\.(?P&lt;designation&gt;.+)\.tmap" ext="tabular" />
+            <filter>annotation['use_ref_annotation'] == 'Yes' and annotation['refmap_tmap'] != None and 'tmap' in annotation['refmap_tmap']</filter>
+        </collection>
     </outputs>
     <tests>
-        <test>
-            <param ftype="gtf" name="inputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" />
+        <test expect_num_outputs="6">
+            <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" />
             <param name="use_ref_annotation" value="Yes" />
-            <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" />
-            <param name="ignore_nonoverlapping_reference" value="Yes" />
-            <param name="ignore_nonoverlapping_transfrags" value="No" />
+            <conditional name="annotation">
+                <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" />
+                <param name="ignore_nonoverlapping_reference" value="Yes" />
+                <param name="ignore_nonoverlapping_transfrags" value="No" />
+            </conditional>
             <param name="use_seq_data" value="No" />
             <param name="discard_single_exon" value="" />
             <param name="max_dist_exon" value="100" />
             <param name="max_dist_group" value="100" />
             <param name="discard_intron_redundant_transfrags" value="No" />
             <output file="gffcompare_out1.stats" name="transcripts_stats" lines_diff="6" />
-            <output file="gffcompare_out1.loci" name="transcripts_loci" />
+            <output file="gffcompare_out1.loci" name="transcripts_loci" lines_diff="2" />
             <output file="gffcompare_out1.tracking" name="transcripts_tracking" />
             <output file="gffcompare_out1.gtf" name="transcripts_combined" />
+            <output_collection name="refmap_output" type="list" count="2">
+                <element name="gffcompare_in1_gtf" file="gffcompare_out1-1.refmap" ftype="tabular" />
+                <element name="gffcompare_in2_gtf" file="gffcompare_out1-2.refmap" ftype="tabular" />
+            </output_collection>
+            <output_collection name="tmap_output" type="list" count="2">
+                <element name="gffcompare_in1_gtf" file="gffcompare_out1-1.tmap" ftype="tabular" />
+                <element name="gffcompare_in2_gtf" file="gffcompare_out1-2.tmap" ftype="tabular" />
+            </output_collection>
         </test>
-        <test>
-            <param ftype="gtf" name="inputs" value="gffcompare_in4.gtf" />
+        <test expect_num_outputs="4">
+            <param ftype="gtf" name="gffinputs" value="gffcompare_in4.gtf" />
             <param name="use_ref_annotation" value="Yes" />
-            <param ftype="gtf" name="reference_annotation" value="gffcompare_in5.gtf" />
-            <param name="ignore_nonoverlapping_reference" value="Yes" />
-            <param name="ignore_nonoverlapping_transfrags" value="No" />
+            <conditional name="annotation">
+                <param ftype="gtf" name="reference_annotation" value="gffcompare_in5.gtf" />
+                <param name="ignore_nonoverlapping_reference" value="Yes" />
+                <param name="ignore_nonoverlapping_transfrags" value="No" />
+                <param name="refmap_tmap" value="" />
+            </conditional>
             <param name="use_seq_data" value="No" />
             <param name="discard_single_exon" value="" />
             <param name="max_dist_exon" value="100" />
             <param name="max_dist_group" value="100" />
             <param name="discard_intron_redundant_transfrags" value="No" />
             <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="6" />
-            <output file="gffcompare_out2.loci" name="transcripts_loci" lines_diff="2" />
+            <output file="gffcompare_out2.loci" name="transcripts_loci" />
             <output file="gffcompare_out2.tracking" name="transcripts_tracking" />
             <output file="gffcompare_out2.gtf" name="transcripts_annotated" />
         </test>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gffcompare_out1-1.refmap	Wed Dec 12 03:19:14 2018 -0500
@@ -0,0 +1,2 @@
+ref_gene_id	ref_id	class_code	qry_id_list
+Xkr4	Xkr4	c	CUFF.13|CUFF.13.1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gffcompare_out1-1.tmap	Wed Dec 12 03:19:14 2018 -0500
@@ -0,0 +1,51 @@
+ref_gene_id	ref_id	class_code	qry_gene_id	qry_id	FMI	FPKM	FPKM_conf_lo	FPKM_conf_hi	cov	len	major_iso_id	ref_match_len
+-	-	u	CUFF.1	CUFF.1.1	100	20.607936	0.000000	49.751960	1.317073	41	CUFF.1.1	-
+-	-	u	CUFF.3	CUFF.3.1	100	27.255658	0.000000	65.800979	1.741935	31	CUFF.3.1	-
+-	-	u	CUFF.5	CUFF.5.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.5.1	-
+-	-	u	CUFF.7	CUFF.7.1	100	9.999117	0.000000	19.998234	0.639053	169	CUFF.7.1	-
+-	-	u	CUFF.9	CUFF.9.1	100	17.776896	9.153835	26.399957	1.136139	404	CUFF.9.1	-
+-	-	u	CUFF.11	CUFF.11.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.11.1	-
+Xkr4	Xkr4	c	CUFF.13	CUFF.13.1	100	10.695258	0.000000	25.820637	0.683544	79	CUFF.13.1	3634
+Xkr4	Xkr4	i	CUFF.15	CUFF.15.1	100	10.695258	0.000000	25.820637	0.683544	79	CUFF.15.1	3634
+Xkr4	Xkr4	i	CUFF.17	CUFF.17.1	100	8.710571	0.000000	21.029179	0.556701	97	CUFF.17.1	3634
+Xkr4	Xkr4	i	CUFF.19	CUFF.19.1	100	29.337687	3.097262	55.578113	1.875000	72	CUFF.19.1	3634
+Xkr4	Xkr4	i	CUFF.21	CUFF.21.1	100	13.851236	0.000000	33.439842	0.885246	61	CUFF.21.1	3634
+Xkr4	Xkr4	i	CUFF.23	CUFF.23.1	100	23.470150	0.000000	50.571145	1.500000	54	CUFF.23.1	3634
+Xkr4	Xkr4	i	CUFF.25	CUFF.25.1	100	14.567679	5.354270	23.781089	0.931034	290	CUFF.25.1	3634
+Xkr4	Xkr4	i	CUFF.27	CUFF.27.1	100	34.253732	0.000000	73.806535	2.189189	37	CUFF.27.1	3634
+-	-	u	CUFF.29	CUFF.29.1	100	107.103219	71.402146	142.804292	6.845070	142	CUFF.29.1	-
+-	-	u	CUFF.31	CUFF.31.1	100	122.650461	40.883487	204.417435	7.838710	31	CUFF.31.1	-
+-	-	u	CUFF.33	CUFF.33.1	100	109.527366	26.732460	192.322273	7.000000	27	CUFF.33.1	-
+-	-	u	CUFF.35	CUFF.35.1	100	96.747183	61.420107	132.074259	6.183206	131	CUFF.35.1	-
+-	-	u	CUFF.37	CUFF.37.1	100	104.085013	53.596365	154.573660	6.652174	69	CUFF.37.1	-
+-	-	u	CUFF.39	CUFF.39.1	100	23.912983	0.000000	51.525317	1.528302	53	CUFF.39.1	-
+-	-	u	CUFF.41	CUFF.41.1	100	10.695258	0.000000	25.820637	0.683544	79	CUFF.41.1	-
+-	-	u	CUFF.43	CUFF.43.1	100	10.561567	0.000000	25.497879	0.675000	80	CUFF.43.1	-
+-	-	u	CUFF.45	CUFF.45.1	100	20.708956	2.186303	39.231609	1.323529	102	CUFF.45.1	-
+-	-	u	CUFF.47	CUFF.47.1	100	20.607936	0.000000	49.751960	1.317073	41	CUFF.47.1	-
+-	-	u	CUFF.49	CUFF.49.1	100	15.646767	0.000000	46.940300	1.000000	27	CUFF.49.1	-
+-	-	u	CUFF.51	CUFF.51.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.51.1	-
+-	-	u	CUFF.53	CUFF.53.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.53.1	-
+-	-	u	CUFF.55	CUFF.55.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.55.1	-
+-	-	u	CUFF.57	CUFF.57.1	100	15.646767	0.000000	46.940300	1.000000	27	CUFF.57.1	-
+-	-	u	CUFF.59	CUFF.59.1	100	15.646767	0.000000	46.940300	1.000000	27	CUFF.59.1	-
+Xkr4	Xkr4	i	CUFF.61	CUFF.61.1	100	45.263860	0.000000	97.530065	2.892857	28	CUFF.61.1	3634
+Xkr4	Xkr4	i	CUFF.63	CUFF.63.1	100	15.646767	0.000000	46.940300	1.000000	27	CUFF.63.1	3634
+Xkr4	Xkr4	i	CUFF.65	CUFF.65.1	100	15.362280	0.000000	37.087825	0.981818	55	CUFF.65.1	3634
+Xkr4	Xkr4	i	CUFF.67	CUFF.67.1	100	12.998852	0.000000	31.382005	0.830769	65	CUFF.67.1	3634
+Xkr4	Xkr4	i	CUFF.69	CUFF.69.1	100	10.058636	0.000000	24.283695	0.642857	84	CUFF.69.1	3634
+Xkr4	Xkr4	i	CUFF.71	CUFF.71.1	100	8.621688	0.000000	20.814595	0.551020	98	CUFF.71.1	3634
+Xkr4	Xkr4	i	CUFF.73	CUFF.73.1	100	15.362280	0.000000	37.087825	0.981818	55	CUFF.73.1	3634
+Xkr4	Xkr4	i	CUFF.75	CUFF.75.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.75.1	3634
+Xkr4	Xkr4	i	CUFF.77	CUFF.77.1	100	16.248565	0.000000	39.227507	1.038462	52	CUFF.77.1	3634
+Xkr4	Xkr4	i	CUFF.79	CUFF.79.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.79.1	3634
+Xkr4	Xkr4	i	CUFF.81	CUFF.81.1	100	13.201959	0.000000	31.872349	0.843750	64	CUFF.81.1	3634
+Xkr4	Xkr4	i	CUFF.83	CUFF.83.1	100	13.201959	0.000000	28.446269	0.843750	96	CUFF.83.1	3634
+Xkr4	Xkr4	i	CUFF.85	CUFF.85.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.85.1	3634
+Xkr4	Xkr4	i	CUFF.87	CUFF.87.1	100	17.243375	0.000000	41.629191	1.102041	49	CUFF.87.1	3634
+Xkr4	Xkr4	i	CUFF.89	CUFF.89.1	100	16.567165	0.000000	39.996674	1.058824	51	CUFF.89.1	3634
+Xkr4	Xkr4	i	CUFF.91	CUFF.91.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.91.1	3634
+Xkr4	Xkr4	i	CUFF.93	CUFF.93.1	100	21.664754	0.000000	52.303342	1.384615	39	CUFF.93.1	3634
+Xkr4	Xkr4	i	CUFF.95	CUFF.95.1	100	46.940300	0.000000	101.142289	3.000000	27	CUFF.95.1	3634
+Xkr4	Xkr4	i	CUFF.97	CUFF.97.1	100	21.481154	0.000000	46.285454	1.372881	59	CUFF.97.1	3634
+Xkr4	Xkr4	i	CUFF.99	CUFF.99.1	100	14.567679	0.000000	35.169489	0.931034	58	CUFF.99.1	3634
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gffcompare_out1-2.refmap	Wed Dec 12 03:19:14 2018 -0500
@@ -0,0 +1,1 @@
+ref_gene_id	ref_id	class_code	qry_id_list
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gffcompare_out1-2.tmap	Wed Dec 12 03:19:14 2018 -0500
@@ -0,0 +1,51 @@
+ref_gene_id	ref_id	class_code	qry_gene_id	qry_id	FMI	FPKM	FPKM_conf_lo	FPKM_conf_hi	cov	len	major_iso_id	ref_match_len
+-	-	u	CUFF.1	CUFF.1.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.1.1	-
+-	-	u	CUFF.3	CUFF.3.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.3.1	-
+-	-	u	CUFF.5	CUFF.5.1	100	21.226627	0.000000	59.889707	1.205672	27	CUFF.5.1	-
+-	-	u	CUFF.7	CUFF.7.1	100	29.709524	19.806349	39.612698	1.687500	576	CUFF.7.1	-
+-	-	u	CUFF.9	CUFF.9.1	100	34.072933	23.364686	44.781179	1.935341	565	CUFF.9.1	-
+-	-	u	CUFF.11	CUFF.11.1	100	32.531777	24.582998	40.480555	1.847804	979	CUFF.11.1	-
+-	-	u	CUFF.13	CUFF.13.1	100	16.582060	0.000000	35.729373	0.941860	86	CUFF.13.1	-
+-	-	u	CUFF.15	CUFF.15.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.15.1	-
+-	-	u	CUFF.17	CUFF.17.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.17.1	-
+-	-	u	CUFF.19	CUFF.19.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.19.1	-
+-	-	u	CUFF.21	CUFF.21.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.21.1	-
+-	-	u	CUFF.23	CUFF.23.1	100	16.205195	0.000000	34.917342	0.920455	88	CUFF.23.1	-
+-	-	u	CUFF.25	CUFF.25.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.25.1	-
+-	-	u	CUFF.26	CUFF.26.1	100	29.709524	0.000000	71.725135	1.687500	32	CUFF.26.1	-
+-	-	u	CUFF.29	CUFF.29.1	100	13.581496	0.000000	32.788633	0.771429	70	CUFF.29.1	-
+-	-	u	CUFF.31	CUFF.31.1	100	22.635827	0.000000	45.271655	1.285714	84	CUFF.31.1	-
+Xkr4	Xkr4	i	CUFF.33	CUFF.33.1	100	23.767619	0.000000	57.380108	1.350000	40	CUFF.33.1	3634
+Xkr4	Xkr4	i	CUFF.35	CUFF.35.1	100	11.317914	0.000000	27.323861	0.642857	84	CUFF.35.1	3634
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