# HG changeset patch
# User fubar2
# Date 1702030496 0
# Node ID 00a0c6edbbb9fe6458b4d6815da27b3203e31c21
# Parent  aff6409d16d126e461e029c0bf9691e12cc1572f
Uploaded

diff -r aff6409d16d1 -r 00a0c6edbbb9 abslen_bed/.shed.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abslen_bed/.shed.yml	Fri Dec 08 10:14:56 2023 +0000
@@ -0,0 +1,6 @@
+category: ToolFactory generated Tools
+description: ToolFactory autogenerated tool
+name: abslen_bed
+owner: fubar2
+synopsis: Returns a file of absolute values from differences
+type: unrestricted
diff -r aff6409d16d1 -r 00a0c6edbbb9 abslen_bed/abslen_bed.python.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abslen_bed/abslen_bed.python.txt	Fri Dec 08 10:14:56 2023 +0000
@@ -0,0 +1,14 @@
+#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
diff -r aff6409d16d1 -r 00a0c6edbbb9 abslen_bed/abslen_bed.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abslen_bed/abslen_bed.xml	Fri Dec 08 10:14:56 2023 +0000
@@ -0,0 +1,56 @@
+<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 08/12/2023 08:58:50 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>
+
diff -r aff6409d16d1 -r 00a0c6edbbb9 abslen_bed/test-data/absin_sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abslen_bed/test-data/absin_sample	Fri Dec 08 10:14:56 2023 +0000
@@ -0,0 +1,4 @@
+mm10_knownGene_uc008xda.1	900	959
+mm10_knownGene_uc008xda.1	1009	1038
+mm10_knownGene_uc008xda.1	1088	1166
+mm10_knownGene_uc008xda.1	1216	1252
diff -r aff6409d16d1 -r 00a0c6edbbb9 abslen_bed/test-data/absout_sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abslen_bed/test-data/absout_sample	Fri Dec 08 10:14:56 2023 +0000
@@ -0,0 +1,4 @@
+mm10_knownGene_uc008xda.1	900	959	59
+mm10_knownGene_uc008xda.1	1009	1038	29
+mm10_knownGene_uc008xda.1	1088	1166	78
+mm10_knownGene_uc008xda.1	1216	1252	36
\ No newline at end of file
diff -r aff6409d16d1 -r 00a0c6edbbb9 absval/.shed.yml
--- a/absval/.shed.yml	Fri Dec 08 08:47:36 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: absval
-owner: fubar2
-synopsis: Returns a file of absolute values from differences
-type: unrestricted
diff -r aff6409d16d1 -r 00a0c6edbbb9 absval/absval.python.txt
--- a/absval/absval.python.txt	Fri Dec 08 08:47:36 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-#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
diff -r aff6409d16d1 -r 00a0c6edbbb9 absval/absval.xml
--- a/absval/absval.xml	Fri Dec 08 08:47:36 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-<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>
-
diff -r aff6409d16d1 -r 00a0c6edbbb9 absval/test-data/absin_sample
diff -r aff6409d16d1 -r 00a0c6edbbb9 absval/test-data/absout_sample