--- a/abslen_bed/.shed.yml	Tue Dec 05 10:34:39 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-category: ToolFactory generated Tools
-description: ToolFactory autogenerated tool
-name: abslen_bed
-owner: fubar2
-synopsis: Add the contig length to the end of each row of a bed file
-type: unrestricted

--- a/abslen_bed/abslen_bed.python.txt	Tue Dec 05 10:34:39 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,14 +0,0 @@
-#raw
-import sys
-inp = []
-for line in sys.stdin:
-    if line.strip() > '':
-        ls = line.split()
-        if len(ls) > 3:
-            x = abs(int(ls[2]) - int(ls[1]))
-            ls.append((str(x)))
-            inp.append('\t'.join(ls))
-    else:
-        break
-sys.stdout.write('\n'.join(inp))
-#end raw

--- a/abslen_bed/abslen_bed.xml	Tue Dec 05 10:34:39 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-<tool name="abslen_bed" id="abslen_bed" version="1" profile="22.05">
-  <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
-  <!--Created by toolfactory@galaxy.org at 05/12/2023 10:23:28 using the Galaxy Tool Factory.-->
-  <description>Add the contig length to the end of each row of a bed file</description>
-  <requirements>
-    <requirement type="package">python</requirement>
-  </requirements>
-  <version_command><![CDATA[echo "1"]]></version_command>
-  <command><![CDATA[python
-'$runme'
-<
-$absin
->
-$absout]]></command>
-  <configfiles>
-    <configfile name="runme"><![CDATA[#raw
-import sys
-inp = []
-for line in sys.stdin:
-    if line.strip() > '':
-        ls = line.split()
-        if len(ls) > 3:
-            x = abs(int(ls[2]) - int(ls[1]))
-            ls.append((str(x)))
-            inp.append('\t'.join(ls))
-    else:
-        break
-sys.stdout.write('\n'.join(inp))
-#end raw]]></configfile>
-  </configfiles>
-  <inputs>
-    <param name="absin" type="data" optional="false" label="absin" help="Input file to be converted using abs()" format="bed" multiple="false"/>
-  </inputs>
-  <outputs>
-    <data name="absout" format="bed" hidden="false"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="absin" value="absin_sample"/>
-      <output name="absout" value="absout_sample"/>
-    </test>
-  </tests>
-  <help><![CDATA[
- Takes absolute values of the differences between the start and end coordinate of each contig in a bed file. 
- This tool is a temporary step to enable the Sanger TreeVal NF gap_finder workflow to be
- translated into Galaxy. Used after seqtk-cutn to make a tabix file of gaps for an assembly.
- 
- See https://github.com/fubar2/treeval_gal/tree/main/gap_finder
-  ]]></help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/bts573</citation>
-  </citations>
-</tool>
-

--- a/abslen_bed/test-data/absin_sample	Tue Dec 05 10:34:39 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-chr1	147962192	147962580	CCDS989.1_cds_0_0_chr1_147962193_r	0	-	chr1	147962192	147962580	NM_005997_cds_0_0_chr1_147962193_r	0	-
-chr1	147984545	147984630	CCDS990.1_cds_0_0_chr1_147984546_f	0	+	chr1	147984545	147984630	BC007833_cds_0_0_chr1_147984546_f	0	+
-chr1	148078400	148078582	CCDS993.1_cds_0_0_chr1_148078401_r	0	-	chr1	148078400	148078582	AJ011123_cds_0_0_chr1_148078401_r	0	-
-chr1	148185136	148185276	CCDS996.1_cds_0_0_chr1_148185137_f	0	+	chr1	148185136	148185276	NM_002796_cds_0_0_chr1_148185137_f	0	+
-chr10	55251623	55253124	CCDS7248.1_cds_0_0_chr10_55251624_r	0	-	chr10	55251623	55253124	AY029205_cds_0_0_chr10_55251624_r	0	-
-chr11	116124407	116124501	CCDS8374.1_cds_0_0_chr11_116124408_r	0	-	chr11	116124407	116124501	AK057832_cds_0_0_chr11_116124408_r	0	-
-chr11	116206508	116206563	CCDS8377.1_cds_0_0_chr11_116206509_f	0	+	chr11	116206508	116206563	NM_000040_cds_1_0_chr11_116206509_f	0	+
-chr11	116211733	116212337	CCDS8378.1_cds_0_0_chr11_116211734_r	0	-	chr11	116211733	116212337	BC005380_cds_0_0_chr11_116211734_r	0	-
-chr12	38440094	38440321	CCDS8736.1_cds_0_0_chr12_38440095_r	0	-	chr12	38440094	38440321	NM_052885_cds_0_0_chr12_38440095_r	0	-
-chr13	112381694	112381953	CCDS9526.1_cds_0_0_chr13_112381695_f	0	+	chr13	112381694	112381953	NM_207440_cds_1_0_chr13_112381695_f	0	+
-chr14	98710240	98712285	CCDS9949.1_cds_0_0_chr14_98710241_r	0	-	chr14	98710240	98712285	NM_022898_cds_0_0_chr14_98710241_r	0	-
-chr15	41486872	41487060	CCDS10096.1_cds_0_0_chr15_41486873_r	0	-	chr15	41486872	41487060	BX537418_cds_0_0_chr15_41486873_r	0	-
-chr15	41673708	41673857	CCDS10097.1_cds_0_0_chr15_41673709_f	0	+	chr15	41673708	41673857	AK223365_cds_0_0_chr15_41673709_f	0	+
-chr15	41679161	41679250	CCDS10098.1_cds_0_0_chr15_41679162_r	0	-	chr15	41679161	41679250	NM_153700_cds_0_0_chr15_41679162_r	0	-
-chr16	142908	143003	CCDS10397.1_cds_0_0_chr16_142909_f	0	+	chr16	142908	143003	NM_005332_cds_0_0_chr16_142909_f	0	+
-chr16	244413	244681	CCDS10402.1_cds_0_0_chr16_244414_f	0	+	chr16	244413	244681	AK057165_cds_2_0_chr16_244414_f	0	+
-chr16	259268	259383	CCDS10403.1_cds_0_0_chr16_259269_r	0	-	chr16	259268	259383	AB016929_cds_0_0_chr16_259269_r	0	-
-chr18	23786114	23786321	CCDS11891.1_cds_0_0_chr18_23786115_r	0	-	chr18	23786114	23786321	NM_001792_cds_0_0_chr18_23786115_r	0	-
-chr18	59406881	59407046	CCDS11985.1_cds_0_0_chr18_59406882_f	0	+	chr18	59406881	59407046	NM_012397_cds_1_0_chr18_59406882_f	0	+
-chr18	59455932	59456337	CCDS11986.1_cds_0_0_chr18_59455933_r	0	-	chr18	59455932	59456337	AB046400_cds_0_0_chr18_59455933_r	0	-
-chr19	59068595	59069564	CCDS12866.1_cds_0_0_chr19_59068596_f	0	+	chr19	59068595	59069564	BC013995_cds_1_0_chr19_59068596_f	0	+
-chr19	59236026	59236146	CCDS12872.1_cds_0_0_chr19_59236027_r	0	-	chr19	59236026	59236146	NM_198481_cds_0_0_chr19_59236027_r	0	-
-chr19	59297998	59298008	CCDS12877.1_cds_0_0_chr19_59297999_f	0	+	chr19	59297998	59298008	NM_004542_cds_0_0_chr19_59297999_f	0	+
-chr2	118288583	118288668	CCDS2120.1_cds_0_0_chr2_118288584_f	0	+	chr2	118288583	118288668	NM_006773_cds_0_0_chr2_118288584_f	0	+
-chr2	220229609	220230869	CCDS2443.1_cds_0_0_chr2_220229610_r	0	-	chr2	220229609	220230869	NM_024536_cds_0_0_chr2_220229610_r	0	-
-chr20	33330413	33330423	CCDS13249.1_cds_0_0_chr20_33330414_r	0	-	chr20	33330413	33330423	NM_181466_cds_0_0_chr20_33330414_r	0	-
-chr20	33513606	33513792	CCDS13255.1_cds_0_0_chr20_33513607_f	0	+	chr20	33513606	33513792	AF022655_cds_1_0_chr20_33513607_f	0	+
-chr21	32869641	32870022	CCDS13615.1_cds_0_0_chr21_32869642_r	0	-	chr21	32869641	32870022	NM_018277_cds_3_0_chr21_32869642_r	0	-
-chr21	33321040	33322012	CCDS13620.1_cds_0_0_chr21_33321041_f	0	+	chr21	33321040	33322012	NM_005806_cds_1_0_chr21_33321041_f	0	+
-chr22	30120223	30120265	CCDS13897.1_cds_0_0_chr22_30120224_f	0	+	chr22	30120223	30120265	NM_004147_cds_0_0_chr22_30120224_f	0	+
-chr22	30160419	30160661	CCDS13898.1_cds_0_0_chr22_30160420_r	0	-	chr22	30160419	30160661	BC032941_cds_0_0_chr22_30160420_r	0	-
-chr5	131424298	131424460	CCDS4149.1_cds_0_0_chr5_131424299_f	0	+	chr5	131424298	131424460	NM_000588_cds_0_0_chr5_131424299_f	0	+
-chr5	131556601	131556672	CCDS4151.1_cds_0_0_chr5_131556602_r	0	-	chr5	131556601	131556672	BC035813_cds_0_0_chr5_131556602_r	0	-
-chr5	131621326	131621419	CCDS4152.1_cds_0_0_chr5_131621327_f	0	+	chr5	131621326	131621419	BC003096_cds_0_0_chr5_131621327_f	0	+
-chr6	108299600	108299744	CCDS5061.1_cds_0_0_chr6_108299601_r	0	-	chr6	108299600	108299744	NM_007214_cds_0_0_chr6_108299601_r	0	-
-chr6	108594662	108594687	CCDS5063.1_cds_0_0_chr6_108594663_f	0	+	chr6	108594662	108594687	NM_003269_cds_0_0_chr6_108594663_f	0	+
-chr6	108640045	108640151	CCDS5064.1_cds_0_0_chr6_108640046_r	0	-	chr6	108640045	108640151	NM_003795_cds_0_0_chr6_108640046_r	0	-
-chr6	108722976	108723115	CCDS5067.1_cds_0_0_chr6_108722977_f	0	+	chr6	108722976	108723115	NM_145315_cds_0_0_chr6_108722977_f	0	+
-chr7	113660517	113660685	CCDS5760.1_cds_0_0_chr7_113660518_f	0	+	chr7	113660517	113660685	AF467257_cds_1_0_chr7_113660518_f	0	+
-chr7	116512159	116512389	CCDS5771.1_cds_0_0_chr7_116512160_r	0	-	chr7	116512159	116512389	NM_003391_cds_0_0_chr7_116512160_r	0	-
-chr7	116714099	116714152	CCDS5773.1_cds_0_0_chr7_116714100_f	0	+	chr7	116714099	116714152	NM_000492_cds_0_0_chr7_116714100_f	0	+
-chr7	116945541	116945787	CCDS5774.1_cds_0_0_chr7_116945542_r	0	-	chr7	116945541	116945787	AF377960_cds_0_0_chr7_116945542_r	0	-
-chr8	118881131	118881317	CCDS6324.1_cds_0_0_chr8_118881132_r	0	-	chr8	118881131	118881317	NM_000127_cds_0_0_chr8_118881132_r	0	-
-chr9	128764156	128764189	CCDS6914.1_cds_0_0_chr9_128764157_f	0	+	chr9	128764156	128764189	BC051300_cds_0_0_chr9_128764157_f	0	+
-chr9	128787519	128789136	CCDS6915.1_cds_0_0_chr9_128787520_r	0	-	chr9	128787519	128789136	NM_014908_cds_0_0_chr9_128787520_r	0	-
-chrX	122745047	122745924	CCDS14606.1_cds_0_0_chrX_122745048_f	0	+	chrX	122745047	122745924	NM_001167_cds_1_0_chrX_122745048_f	0	+
-chrX	152648964	152649196	CCDS14733.1_cds_0_0_chrX_152648965_r	0	-	chrX	152648964	152649196	NM_000425_cds_0_0_chrX_152648965_r	0	-
-chrX	152691446	152691471	CCDS14735.1_cds_0_0_chrX_152691447_f	0	+	chrX	152691446	152691471	AF101728_cds_0_0_chrX_152691447_f	0	+
-chrX	152694029	152694263	CCDS14736.1_cds_0_0_chrX_152694030_r	0	-	chrX	152694029	152694263	BC052303_cds_0_0_chrX_152694030_r	0	-

--- a/abslen_bed/test-data/absout_sample	Tue Dec 05 10:34:39 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-chr1	147962192	147962580	region_0	0	-	388
-chr1	147984545	147984630	region_1	0	+	85
-chr1	148078400	148078582	region_2	0	-	182
-chr1	148185136	148185276	region_3	0	+	140
-chr10	55251623	55253124	region_4	0	-	1501
-chr11	116124407	116124501	region_5	0	-	94
-chr11	116206508	116206563	region_6	0	+	55
-chr11	116211733	116212337	region_7	0	-	604
-chr12	38440094	38440321	region_8	0	-	227
-chr13	112381694	112381953	region_9	0	+	259
-chr14	98710240	98712285	region_10	0	-	2045
-chr15	41486872	41487060	region_11	0	-	188
-chr15	41673708	41673857	region_12	0	+	149
-chr15	41679161	41679250	region_13	0	-	89
-chr16	142908	143003	region_14	0	+	95
-chr16	244413	244681	region_15	0	+	268
-chr16	259268	259383	region_16	0	-	115
-chr18	23786114	23786321	region_17	0	-	207
-chr18	59406881	59407046	region_18	0	+	165
-chr18	59455932	59456337	region_19	0	-	405
-chr19	59068595	59069564	region_20	0	+	969
-chr19	59236026	59236146	region_21	0	-	120
-chr19	59297998	59298008	region_22	0	+	10
-chr2	118288583	118288668	region_23	0	+	85
-chr2	220229609	220230869	region_24	0	-	1260
-chr20	33330413	33330423	region_25	0	-	10
-chr20	33513606	33513792	region_26	0	+	186
-chr21	32869641	32870022	region_27	0	-	381
-chr21	33321040	33322012	region_28	0	+	972
-chr22	30120223	30120265	region_29	0	+	42
-chr22	30160419	30160661	region_30	0	-	242
-chr5	131424298	131424460	region_31	0	+	162
-chr5	131556601	131556672	region_32	0	-	71
-chr5	131621326	131621419	region_33	0	+	93
-chr6	108299600	108299744	region_34	0	-	144
-chr6	108594662	108594687	region_35	0	+	25
-chr6	108640045	108640151	region_36	0	-	106
-chr6	108722976	108723115	region_37	0	+	139
-chr7	113660517	113660685	region_38	0	+	168
-chr7	116512159	116512389	region_39	0	-	230
-chr7	116714099	116714152	region_40	0	+	53
-chr7	116945541	116945787	region_41	0	-	246
-chr8	118881131	118881317	region_42	0	-	186
-chr9	128764156	128764189	region_43	0	+	33
-chr9	128787519	128789136	region_44	0	-	1617
-chrX	122745047	122745924	region_45	0	+	877
-chrX	152648964	152649196	region_46	0	-	232
-chrX	152691446	152691471	region_47	0	+	25
-chrX	152694029	152694263	region_48	0	-	234
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/absval/.shed.yml	Fri Dec 08 08:47:36 2023 +0000
@@ -0,0 +1,6 @@
+category: ToolFactory generated Tools
+description: ToolFactory autogenerated tool
+name: absval
+owner: fubar2
+synopsis: Returns a file of absolute values from differences
+type: unrestricted

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/absval/absval.python.txt	Fri Dec 08 08:47:36 2023 +0000
@@ -0,0 +1,11 @@
+#raw
+import sys
+inp = []
+for line in sys.stdin:
+    if line.strip() > '':
+        x = line.split()[0]
+        inp.append(str(abs(float(x))))
+    else:
+        break
+sys.stdout.write('\n'.join(inp))
+#end raw

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/absval/absval.xml	Fri Dec 08 08:47:36 2023 +0000
@@ -0,0 +1,56 @@
+<tool name="absval" id="absval" version="1" profile="22.05">
+  <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
+  <!--Created by toolfactory@galaxy.org at 08/12/2023 08:31:05 using the Galaxy Tool Factory.-->
+  <description>Returns a file of absolute values from differences</description>
+  <requirements>
+    <requirement type="package">python</requirement>
+  </requirements>
+  <version_command><![CDATA[echo "1"]]></version_command>
+  <command><![CDATA[python
+'$runme'
+<
+$absin
+>
+$absout]]></command>
+  <configfiles>
+    <configfile name="runme"><![CDATA[#raw
+import sys
+inp = []
+for line in sys.stdin:
+    if line.strip() > '':
+        ls = line.split()
+        if len(ls) > 2:
+            x = abs(int(ls[2]) - int(ls[1]))
+            ls.append((str(x)))
+            inp.append('\t'.join(ls))
+    else:
+        break
+sys.stdout.write('\n'.join(inp))
+#end raw]]></configfile>
+  </configfiles>
+  <inputs>
+    <param name="absin" type="data" optional="false" label="absin" help="Input file to be converted using abs()" format="csfasta,txt,tabular" multiple="false"/>
+  </inputs>
+  <outputs>
+    <data name="absout" format="txt" hidden="false"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="absin" value="absin_sample"/>
+      <output name="absout" value="absout_sample"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+ **What it Does**
+ Takes absolute values on the input 
+ 
+ This tool is a temporary step to enable the Sanger TreeVal NF gap_finder workflow to be
+ translated into Galaxy
+ 
+ See https://github.com/fubar2/treeval_gal/tree/main/gap_finder
+  ]]></help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/bts573</citation>
+  </citations>
+</tool>
+