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changeset 62:881bd8c81ac9 draft

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Uploaded
author fubar
date Mon, 26 Oct 2020 02:51:54 +0000
parents dc923f16e6ff
children b3254219d4fb
files toolfactory/rgToolFactory2.py toolfactory/rgToolFactory2.xml toolfactory/test-data/input1_sample toolfactory/test-data/output2_sample toolfactory/test-data/pyrevpos.python toolfactory/test-data/test1_log.txt toolfactory/test-data/toolfactory_pyrevpos_tgz_sample toolfactory/tool_dependencies.xml
diffstat 8 files changed, 405 insertions(+), 56 deletions(-) [+]
line wrap: on
line diff
--- a/toolfactory/rgToolFactory2.py	Thu Oct 22 03:39:09 2020 +0000
+++ b/toolfactory/rgToolFactory2.py	Mon Oct 26 02:51:54 2020 +0000
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # rgToolFactory.py
 # see https://github.com/fubar2/toolfactory
 #
@@ -325,15 +324,18 @@
         """ no parameters - uses < and > for i/o
         """
         aCL = self.cl.append
-        aCL("<")
-        aCL(self.infiles[0][IPATHPOS])
-        aCL(">")
-        aCL(self.outfiles[0][OCLPOS])
         aXCL = self.xmlcl.append
-        aXCL("<")
-        aXCL("$%s" % self.infiles[0][ICLPOS])
-        aXCL(">")
-        aXCL("$%s" % self.outfiles[0][ONAMEPOS])
+
+        if len(self.infiles) > 0:
+            aCL("<")
+            aCL(self.infiles[0][IPATHPOS])
+            aXCL("<")
+            aXCL("$%s" % self.infiles[0][ICLPOS])
+        if len(self.outfiles) > 0:
+            aCL(">")
+            aCL(self.outfiles[0][OCLPOS])
+            aXCL(">")
+            aXCL("$%s" % self.outfiles[0][ONAMEPOS])
 
     def clpositional(self):
         # inputs in order then params
@@ -482,37 +484,39 @@
 
     def doNoXMLparam(self):
         """filter style package - stdin to stdout"""
-        alab = self.infiles[0][ILABPOS]
-        if len(alab) == 0:
-            alab = self.infiles[0][ICLPOS]
-        max1s = (
-            "Maximum one input if parampass is 0 but multiple input files supplied - %s"
-            % str(self.infiles)
-        )
-        assert len(self.infiles) == 1, max1s
-        newname = self.infiles[0][ICLPOS]
-        aninput = gxtp.DataParam(
-            newname,
-            optional=False,
-            label=alab,
-            help=self.infiles[0][IHELPOS],
-            format=self.infiles[0][IFMTPOS],
-            multiple=False,
-            num_dashes=0,
-        )
-        aninput.command_line_override = "< $%s" % newname
-        aninput.positional = self.is_positional
-        self.tinputs.append(aninput)
-        tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
-        self.testparam.append(tp)
-        newname = self.outfiles[0][OCLPOS]
-        newfmt = self.outfiles[0][OFMTPOS]
-        anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
-        anout.command_line_override = "> $%s" % newname
-        anout.positional = self.is_positional
-        self.toutputs.append(anout)
-        tp = gxtp.TestOutput(name=newname, value="%s_sample" % newname, format=newfmt)
-        self.testparam.append(tp)
+        if len(self.infiles) > 0:
+            alab = self.infiles[0][ILABPOS]
+            if len(alab) == 0:
+                alab = self.infiles[0][ICLPOS]
+            max1s = (
+                "Maximum one input if parampass is 0 but multiple input files supplied - %s"
+                % str(self.infiles)
+            )
+            assert len(self.infiles) == 1, max1s
+            newname = self.infiles[0][ICLPOS]
+            aninput = gxtp.DataParam(
+                newname,
+                optional=False,
+                label=alab,
+                help=self.infiles[0][IHELPOS],
+                format=self.infiles[0][IFMTPOS],
+                multiple=False,
+                num_dashes=0,
+            )
+            aninput.command_line_override = "< $%s" % newname
+            aninput.positional = self.is_positional
+            self.tinputs.append(aninput)
+            tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
+            self.testparam.append(tp)
+        if len(self.outfiles > 0):
+            newname = self.outfiles[0][OCLPOS]
+            newfmt = self.outfiles[0][OFMTPOS]
+            anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
+            anout.command_line_override = "> $%s" % newname
+            anout.positional = self.is_positional
+            self.toutputs.append(anout)
+            tp = gxtp.TestOutput(name=newname, value="%s_sample" % newname, format=newfmt)
+            self.testparam.append(tp)
 
     def makeXML(self):
         """
@@ -529,13 +533,13 @@
             safertext = [html_escape(x) for x in helptext]
             if self.args.script_path:
                 scrpt = self.script.split('\n')
-                scrpt.append("```\n")
+                scrpt.insert(0,"```\n")
                 if len(scrpt) > 300:
                     safertext = safertext + scrpt[:100] + ['>500 lines - stuff deleted','......'] + scrpt[-100:]
                 else:
                     safertext = safertext + scrpt
                 safertext.append("\n```")
-            self.newtool.help = "".join([x for x in safertext])
+            self.newtool.help = "\n".join([x for x in safertext])
         else:
             self.newtool.help = (
                 "Please ask the tool author (%s) for help \
@@ -627,8 +631,14 @@
             ste.close()
             retval = p.returncode
         else:  # work around special case - stdin and write to stdout
-            sti = open(self.infiles[0][IPATHPOS], "rb")
-            sto = open(self.outfiles[0][ONAMEPOS], "wb")
+            if len(self.infiles) > 0:
+                sti = open(self.infiles[0][IPATHPOS], "rb")
+            else:
+                sti = sys.stdin    
+            if len(self.outfiles) > 0:
+                sto = open(self.outfiles[0][ONAMEPOS], "wb")
+            else:
+                sto = sys.stdout
             p = subprocess.run(self.cl, shell=False, stdout=sto, stdin=sti)
             retval = p.returncode
             sto.close()
@@ -695,7 +705,6 @@
             cll = [
                 "planemo",
                 "test",
-                "--skip_venv",
                 "--galaxy_root",
                 self.args.galaxy_root,
                 "--update_test_data",
@@ -703,7 +712,7 @@
             ]
         else:
             cll = ["planemo", "test", "--galaxy_root",
-                self.args.galaxy_root, "--skip_venv",
+                self.args.galaxy_root, 
                 xreal,]
         p = subprocess.run(
                 cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout
--- a/toolfactory/rgToolFactory2.xml	Thu Oct 22 03:39:09 2020 +0000
+++ b/toolfactory/rgToolFactory2.xml	Mon Oct 26 02:51:54 2020 +0000
@@ -1,5 +1,5 @@
-<tool id="rgTF2" name="toolfactory" version="2.01" profile="16.04" >
-  <description>Scripts into tools v2.01</description>
+<tool id="rgtf2" name="toolfactory" version="2.01" profile="16.04" >
+  <description>Scripts into tools v2.0</description>
   <macros>
      <xml name="tool_metadata">
          <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
@@ -132,7 +132,8 @@
   </macros>
 
 <requirements>
-       <requirement type="package" version="0.01" >tfdeps</requirement>
+       <requirement type="package" version="0.72.0" >planemo</requirement>
+       <requirement type="package" version="0.4.11" >galaxyxml</requirement>
 </requirements>
   
   <command ><![CDATA[
@@ -330,7 +331,7 @@
         <when value="generate">
             <expand macro="tool_metadata" />
         </when>
-        <when value="gentest">
+       <when value="gentest">
             <expand macro="tool_metadata" />
         </when>
        <when value="gentestinstall">
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/test-data/input1_sample	Mon Oct 26 02:51:54 2020 +0000
@@ -0,0 +1,166 @@
+*WARNING before you start*
+
+ Install this tool on a private Galaxy ONLY
+ Please NEVER on a public or production instance
+ 
+Updated august 2014 by John Chilton adding citation support
+
+Updated august 8 2014 to fix bugs reported by Marius van den Beek
+
+Please cite the resource at
+http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
+if you use this tool in your published work.
+
+**Short Story**
+
+This is an unusual Galaxy tool capable of generating new Galaxy tools.
+It works by exposing *unrestricted* and therefore extremely dangerous scripting
+to all designated administrators of the host Galaxy server, allowing them to
+run scripts in R, python, sh and perl over multiple selected input data sets,
+writing a single new data set as output.
+
+*You have a working r/python/perl/bash script or any executable with positional or argparse style parameters*
+
+It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool.
+
+
+**Automated generation of new Galaxy tools for installation into any Galaxy**
+
+A test is generated using small sample test data inputs and parameter settings you supply.
+Once the test case outputs have been produced, they can be used to build a
+new Galaxy tool. The supplied script or executable is baked as a requirement
+into a new, ordinary Galaxy tool, fully workflow compatible out of the box.
+Generated tools are installed via a tool shed by an administrator
+and work exactly like all other Galaxy tools for your users.
+
+**More Detail**
+
+To use the ToolFactory, you should have prepared a script to paste into a
+text box, or have a package in mind and a small test input example ready to select from your history
+to test your new script.
+
+```planemo test rgToolFactory2.xml --galaxy_root ~/galaxy --test_data ~/galaxy/tools/tool_makers/toolfactory/test-data``` works for me
+
+There is an example in each scripting language on the Tool Factory form. You
+can just cut and paste these to try it out - remember to select the right
+interpreter please. You'll also need to create a small test data set using
+the Galaxy history add new data tool.
+
+If the script fails somehow, use the "redo" button on the tool output in
+your history to recreate the form complete with broken script. Fix the bug
+and execute again. Rinse, wash, repeat.
+
+Once the script runs sucessfully, a new Galaxy tool that runs your script
+can be generated. Select the "generate" option and supply some help text and
+names. The new tool will be generated in the form of a new Galaxy datatype
+*toolshed.gz* - as the name suggests, it's an archive ready to upload to a
+Galaxy ToolShed as a new tool repository.
+
+Once it's in a ToolShed, it can be installed into any local Galaxy server
+from the server administrative interface.
+
+Once the new tool is installed, local users can run it - each time, the script
+that was supplied when it was built will be executed with the input chosen
+from the user's history. In other words, the tools you generate with the
+ToolFactory run just like any other Galaxy tool,but run your script every time.
+
+Tool factory tools are perfect for workflow components. One input, one output,
+no variables.
+
+*To fully and safely exploit the awesome power* of this tool,
+Galaxy and the ToolShed, you should be a developer installing this
+tool on a private/personal/scratch local instance where you are an
+admin_user. Then, if you break it, you get to keep all the pieces see
+https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
+
+**Installation**
+This is a Galaxy tool. You can install it most conveniently using the
+administrative "Search and browse tool sheds" link. Find the Galaxy Main
+toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory
+repository. Open it and review the code and select the option to install it.
+
+If you can't get the tool that way, the xml and py files here need to be
+copied into a new tools
+subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry
+pointing to the xml
+file - something like::
+
+  <section name="Tool building tools" id="toolbuilders">
+    <tool file="toolfactory/rgToolFactory.xml"/>
+  </section>
+
+If not already there,
+please add:
+<datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary"
+mimetype="multipart/x-gzip" subclass="True" />
+to your local data_types_conf.xml.
+
+
+**Restricted execution**
+
+The tool factory tool itself will then be usable ONLY by admin users -
+people with IDs in admin_users in universe_wsgi.ini **Yes, that's right. ONLY
+admin_users can run this tool** Think about it for a moment. If allowed to
+run any arbitrary script on your Galaxy server, the only thing that would
+impede a miscreant bent on destroying all your Galaxy data would probably
+be lack of appropriate technical skills.
+
+**What it does** 
+
+This is a tool factory for simple scripts in python, R and
+perl currently. Functional tests are automatically generated. How cool is that.
+
+LIMITED to simple scripts that read one input from the history. Optionally can
+write one new history dataset, and optionally collect any number of outputs
+into links on an autogenerated HTML index page for the user to navigate -
+useful if the script writes images and output files - pdf outputs are shown
+as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and
+imagemagik need to be available.
+
+Generated tools can be edited and enhanced like any Galaxy tool, so start
+small and build up since a generated script gets you a serious leg up to a
+more complex one.
+
+**What you do**
+
+You paste and run your script, you fix the syntax errors and
+eventually it runs. You can use the redo button and edit the script before
+trying to rerun it as you debug - it works pretty well.
+
+Once the script works on some test data, you can generate a toolshed compatible
+gzip file containing your script ready to run as an ordinary Galaxy tool in
+a repository on your local toolshed. That means safe and largely automated
+installation in any production Galaxy configured to use your toolshed.
+
+**Generated tool Security**
+
+Once you install a generated tool, it's just
+another tool - assuming the script is safe. They just run normally and their
+user cannot do anything unusually insecure but please, practice safe toolshed.
+Read the code before you install any tool. Especially this one - it is really scary.
+
+**Send Code**
+
+Patches and suggestions welcome as bitbucket issues please?
+
+**Attribution**
+
+Creating re-usable tools from scripts: The Galaxy Tool Factory
+Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team
+Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
+
+http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
+
+**Licensing**
+
+Copyright Ross Lazarus 2010
+ross lazarus at g mail period com
+
+All rights reserved.
+
+Licensed under the LGPL
+
+**Obligatory screenshot**
+
+http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/test-data/output2_sample	Mon Oct 26 02:51:54 2020 +0000
@@ -0,0 +1,165 @@
+*trats uoy erofeb GNINRAW*
+
+YLNO yxalaG etavirp a no loot siht llatsnI 
+ecnatsni noitcudorp ro cilbup a no REVEN esaelP 
+
+troppus noitatic gnidda notlihC nhoJ yb 4102 tsugua detadpU
+
+keeB ned nav suiraM yb detroper sgub xif ot 4102 8 tsugua detadpU
+
+ta ecruoser eht etic esaelP
+fer=epytyek&JWYdwMrWs1hQzcl=yekji?375stb/tnirper/igc/gro.slanruojdrofxo.scitamrofnioib//:ptth
+.krow dehsilbup ruoy ni loot siht esu uoy fi
+
+**yrotS trohS**
+
+.sloot yxalaG wen gnitareneg fo elbapac loot yxalaG lausunu na si sihT
+gnitpircs suoregnad ylemertxe erofereht dna *detcirtsernu* gnisopxe yb skrow tI
+ot meht gniwolla ,revres yxalaG tsoh eht fo srotartsinimda detangised lla ot
+,stes atad tupni detceles elpitlum revo lrep dna hs ,nohtyp ,R ni stpircs nur
+.tuptuo sa tes atad wen elgnis a gnitirw
+
+*sretemarap elyts esrapgra ro lanoitisop htiw elbatucexe yna ro tpircs hsab/lrep/nohtyp/r gnikrow a evah uoY*
+
+.loot yxalaG a gnisu ,setunim ni loot yxalaG yranidro na otni denrut eb nac tI
+
+
+**yxalaG yna otni noitallatsni rof sloot yxalaG wen fo noitareneg detamotuA**
+
+.ylppus uoy sgnittes retemarap dna stupni atad tset elpmas llams gnisu detareneg si tset A
+a dliub ot desu eb nac yeht ,decudorp neeb evah stuptuo esac tset eht ecnO
+tnemeriuqer a sa dekab si elbatucexe ro tpircs deilppus ehT .loot yxalaG wen
+.xob eht fo tuo elbitapmoc wolfkrow ylluf ,loot yxalaG yranidro ,wen a otni
+rotartsinimda na yb dehs loot a aiv dellatsni era sloot detareneG
+.sresu ruoy rof sloot yxalaG rehto lla ekil yltcaxe krow dna
+
+**liateD eroM**
+
+a otni etsap ot tpircs a deraperp evah dluohs uoy ,yrotcaFlooT eht esu oT
+yrotsih ruoy morf tceles ot ydaer elpmaxe tupni tset llams a dna dnim ni egakcap a evah ro ,xob txet
+.tpircs wen ruoy tset ot
+
+em rof skrow ```atad-tset/yrotcafloot/srekam_loot/sloot/yxalag/~ atad_tset-- yxalag/~ toor_yxalag-- lmx.2yrotcaFlooTgr tset omenalp```
+
+uoY .mrof yrotcaF looT eht no egaugnal gnitpircs hcae ni elpmaxe na si erehT
+thgir eht tceles ot rebmemer - tuo ti yrt ot eseht etsap dna tuc tsuj nac
+gnisu tes atad tset llams a etaerc ot deen osla ll'uoY .esaelp reterpretni
+.loot atad wen dda yrotsih yxalaG eht
+
+ni tuptuo loot eht no nottub "oder" eht esu ,wohemos sliaf tpircs eht fI
+gub eht xiF .tpircs nekorb htiw etelpmoc mrof eht etaercer ot yrotsih ruoy
+.taeper ,hsaw ,esniR .niaga etucexe dna
+
+tpircs ruoy snur taht loot yxalaG wen a ,yllufssecus snur tpircs eht ecnO
+dna txet pleh emos ylppus dna noitpo "etareneg" eht tceleS .detareneg eb nac
+epytatad yxalaG wen a fo mrof eht ni detareneg eb lliw loot wen ehT .seman
+a ot daolpu ot ydaer evihcra na s'ti ,stseggus eman eht sa - *zg.dehsloot*
+.yrotisoper loot wen a sa dehSlooT yxalaG
+
+revres yxalaG lacol yna otni dellatsni eb nac ti ,dehSlooT a ni s'ti ecnO
+.ecafretni evitartsinimda revres eht morf
+
+tpircs eht ,emit hcae - ti nur nac sresu lacol ,dellatsni si loot wen eht ecnO
+nesohc tupni eht htiw detucexe eb lliw tliub saw ti nehw deilppus saw taht
+eht htiw etareneg uoy sloot eht ,sdrow rehto nI .yrotsih s'resu eht morf
+.emit yreve tpircs ruoy nur tub,loot yxalaG rehto yna ekil tsuj nur yrotcaFlooT
+
+,tuptuo eno ,tupni enO .stnenopmoc wolfkrow rof tcefrep era sloot yrotcaf looT
+.selbairav on
+
+,loot siht fo *rewop emosewa eht tiolpxe ylefas dna ylluf oT*
+siht gnillatsni repoleved a eb dluohs uoy ,dehSlooT eht dna yxalaG
+na era uoy erehw ecnatsni lacol hctarcs/lanosrep/etavirp a no loot
+ees seceip eht lla peek ot teg uoy ,ti kaerb uoy fi ,nehT .resu_nimda
+emoH/ikiw/yrotcaflootyxalag/rabuf/gro.tekcubtib//:sptth
+
+**noitallatsnI**
+eht gnisu yltneinevnoc tsom ti llatsni nac uoY .loot yxalaG a si sihT
+niaM yxalaG eht dniF .knil "sdehs loot esworb dna hcraeS" evitartsinimda
+yrotcafloot eht rof hcraes dna /ude.usp.xb.2g.dehsloot//:sptth ta dehsloot
+.ti llatsni ot noitpo eht tceles dna edoc eht weiver dna ti nepO .yrotisoper
+
+eb ot deen ereh selif yp dna lmx eht ,yaw taht loot eht teg t'nac uoy fI
+sloot wen a otni deipoc
+yrtne wen a sdeen lmx.fnoc_loot ruoY yrotcafloot/sloot sa hcus yrotceridbus
+lmx eht ot gnitniop
+::ekil gnihtemos - elif
+
+>"sredliubloot"=di "sloot gnidliub looT"=eman noitces<  
+>/"lmx.yrotcaFlooTgr/yrotcafloot"=elif loot<    
+>noitces/<  
+
+,ereht ydaerla ton fI
+:dda esaelp
+"yraniB:yranib.sepytatad.yxalag"=epyt "zg.dehsloot"=noisnetxe epytatad<
+>/ "eurT"=ssalcbus "pizg-x/trapitlum"=epytemim
+.lmx.fnoc_sepyt_atad lacol ruoy ot
+
+
+**noitucexe detcirtseR**
+
+- sresu nimda yb YLNO elbasu eb neht lliw flesti loot yrotcaf loot ehT
+YLNO .thgir s'taht ,seY** ini.igsw_esrevinu ni sresu_nimda ni sDI htiw elpoep
+ot dewolla fI .tnemom a rof ti tuoba knihT **loot siht nur nac sresu_nimda
+dluow taht gniht ylno eht ,revres yxalaG ruoy no tpircs yrartibra yna nur
+ylbaborp dluow atad yxalaG ruoy lla gniyortsed no tneb tnaercsim a edepmi
+.slliks lacinhcet etairporppa fo kcal eb
+
+**seod ti tahW**
+
+dna R ,nohtyp ni stpircs elpmis rof yrotcaf loot a si sihT
+.taht si looc woH .detareneg yllacitamotua era stset lanoitcnuF .yltnerruc lrep
+
+nac yllanoitpO .yrotsih eht morf tupni eno daer taht stpircs elpmis ot DETIMIL
+stuptuo fo rebmun yna tcelloc yllanoitpo dna ,tesatad yrotsih wen eno etirw
+- etagivan ot resu eht rof egap xedni LMTH detarenegotua na no sknil otni
+nwohs era stuptuo fdp - selif tuptuo dna segami setirw tpircs eht fi lufesu
+dna taht os tpircstsohg htiw knurhs era s'fdp detaolb s'R dna slianbmuht sa
+.elbaliava eb ot deen kigamegami
+
+trats os ,loot yxalaG yna ekil decnahne dna detide eb nac sloot detareneG
+a ot pu gel suoires a uoy steg tpircs detareneg a ecnis pu dliub dna llams
+.eno xelpmoc erom
+
+**od uoy tahW**
+
+dna srorre xatnys eht xif uoy ,tpircs ruoy nur dna etsap uoY
+erofeb tpircs eht tide dna nottub oder eht esu nac uoY .snur ti yllautneve
+.llew ytterp skrow ti - gubed uoy sa ti nurer ot gniyrt
+
+elbitapmoc dehsloot a etareneg nac uoy ,atad tset emos no skrow tpircs eht ecnO
+ni loot yxalaG yranidro na sa nur ot ydaer tpircs ruoy gniniatnoc elif pizg
+detamotua ylegral dna efas snaem tahT .dehsloot lacol ruoy no yrotisoper a
+.dehsloot ruoy esu ot derugifnoc yxalaG noitcudorp yna ni noitallatsni
+
+**ytiruceS loot detareneG**
+
+tsuj s'ti ,loot detareneg a llatsni uoy ecnO
+rieht dna yllamron nur tsuj yehT .efas si tpircs eht gnimussa - loot rehtona
+.dehsloot efas ecitcarp ,esaelp tub erucesni yllausunu gnihtyna od tonnac resu
+.yracs yllaer si ti - eno siht yllaicepsE .loot yna llatsni uoy erofeb edoc eht daeR
+
+**edoC dneS**
+
+?esaelp seussi tekcubtib sa emoclew snoitseggus dna sehctaP
+
+**noitubirttA**
+
+yrotcaF looT yxalaG ehT :stpircs morf sloot elbasu-er gnitaerC
+maeT yxalaG ehT ;nnameiZ kraM ;ipsaK ynotnA ;surazaL ssoR
+375stb/scitamrofnioib/3901.01 :iod ;2102 scitamrofnioiB
+
+fer=epytyek&JWYdwMrWs1hQzcl=yekji?375stb/tnirper/igc/gro.slanruojdrofxo.scitamrofnioib//:ptth
+
+**gnisneciL**
+
+0102 surazaL ssoR thgirypoC
+moc doirep liam g ta surazal ssor
+
+.devreser sthgir llA
+
+LPGL eht rednu desneciL
+
+**tohsneercs yrotagilbO**
+
+gnp.looTtpircScimanyd/segami/989ef2308adf/crs/rekamlootyxalag/rabuf/gro.tekcubtib//:ptth
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/test-data/pyrevpos.python	Mon Oct 26 02:51:54 2020 +0000
@@ -0,0 +1,13 @@
+# reverse order of text by row
+import sys
+inp = sys.argv[1]
+outp = sys.argv[2]
+i = open(inp,'r').readlines()
+o = open(outp,'w')
+for row in i:
+   rs = row.rstrip()
+   rs = list(rs)
+   rs.reverse()
+   o.write(''.join(rs))
+o.close() 
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/test-data/test1_log.txt	Mon Oct 26 02:51:54 2020 +0000
@@ -0,0 +1,1 @@
+## Executing Toolfactory generated command line = python /tmp/pyrevposq5dmcdy1.python /tmp/tmpqrksf8sd/files/5/b/9/dataset_5b952a86-87df-44ad-a415-ea549f3f0cee.dat output2
Binary file toolfactory/test-data/toolfactory_pyrevpos_tgz_sample has changed
--- a/toolfactory/tool_dependencies.xml	Thu Oct 22 03:39:09 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0" ?>
-<tool_dependency>
-    <package name="tfdeps" version="0.01">
-        <repository name="toolfactory_deps_01" owner="fubar" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="d83a40878d01"/>
-    </package>
-</tool_dependency>
\ No newline at end of file