--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/LICENSE	Thu Jul 01 05:52:07 2021 +0000
@@ -0,0 +1,504 @@
+GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 2.1, February 1999
+
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+That's all there is to it!

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolfactory/README.md	Thu Jul 01 05:52:07 2021 +0000
@@ -0,0 +1,378 @@
+## Breaking news! Completely refactored
+
+### New demonstration of planemo tool_factory command ![Planemo ToolFactory demonstration](images/lintplanemo-2021-01-08_18.02.45.mkv?raw=false "Demonstration inside Planemo")
+
+# WARNING
+
+Install this tool to a throw-away private Galaxy or Docker container ONLY!
+
+Please NEVER on a public or production instance where a hostile user may
+be able to gain access if they can acquire an administrative account login.
+
+It only runs for server administrators - the ToolFactory tool will refuse to execute for an ordinary user since
+it can install new tools to the Galaxy server it executes on! This is not something you should allow other than
+on a throw away instance that is protected from potentially hostile users.
+
+## Short Story
+
+Galaxy is easily extended to new applications by adding a new tool. Each new scientific computational package added as
+a tool to Galaxy requires an XML document describing how the application interacts with Galaxy.
+This is sometimes termed "wrapping" the package because the instructions tell Galaxy how to run the package
+as a new Galaxy tool. Any tool that has been wrapped is readily available to all the users through a consistent
+and easy to use interface once installed in the local Galaxy server.
+
+Most Galaxy tool wrappers have been manually prepared by skilled programmers, many using Planemo because it
+automates much of the boilerplate and makes the process much easier.
+The ToolFactory (TF) now uses Planemo under the hood for testing, but hides the command
+line complexities. The user will still need appropriate skills in terms of describing the interface between
+Galaxy and the new application, but will be helped by a Galaxy tool form to collect all the needed
+settings, together with automated testing and uploading to a toolshed with optional local installation.
+
+
+## ToolFactory generated tools are ordinary Galaxy tools
+
+A TF generated tool that passes the Planemo test is ready to publish in any Galaxy Toolshed and ready to install in any running Galaxy instance.
+They are fully workflow compatible and work exactly like any hand-written tool. The user can select input files of the specified type(s) from their
+history and edit each of the specified parameters. The tool form will show all the labels and help text supplied when the tool was built. When the tool
+is executed, the dependent binary or script will be passed all the i/o files and parameters as specified, and will write outputs to the specified new
+history datasets - just like any other Galaxy tool.
+
+## Models for tool command line construction
+
+The key to turning any software package into a Galaxy tool is the automated construction of a suitable command line.
+
+The TF can build a new tool that will allow the tool user to select input files from their history, set any parameters and when run will send the
+new output files to the history as specified when the tool builder completed the form and built the new tool.
+
+That tool can contain instructions to run any Conda dependency or a system executable like bash. Whether a bash script you have written or
+a Conda package like bwa, the executable will expect to find settings for input, output and parameters on a command line.
+
+These are often passed as "--name value" (argparse style) or in a fixed order (positional style).
+
+The ToolFactory allows either, or for "filter" applications that process input from STDIN and write processed output to STDOUT.
+
+The simplest tool model wraps a simple script or Conda dependency package requiring only input and output files, with no user supplied settings illustrated by
+the Tacrev demonstration tool found in the Galaxy running in the ToolFactory docker container. It passes a user selected input file from the current history on STDIN
+to a bash script. The bash script runs the unix tac utility (reverse cat) piped to the unix rev (reverse lines in a text file) utility. It's a one liner:
+
+`tac | rev`
+
+The tool building form allows zero or more Conda package name(s) and version(s) and an optional script to be executed by either a system
+executable like ``bash`` or the first of any named Conda dependency package/version. Tacrev uses a tiny bash script shown above and uses the system
+bash. Conda bash can be specified if it is important to use the same version consistently for the tool.
+
+On the tool form, the repeat section allowing zero or more input files was set to be a text file to be selected by the tool user and
+in the repeat section allowing one or more outputs, a new output file with special value `STDOUT` as the positional parameter, causes the TF to
+generate a command to capture STDOUT and send it to the new history file containing the reversed input text.
+
+By reversed, we mean really, truly reversed.
+
+That simple model can be made much more complicated, and can pass inputs and outputs as named or positional parameters,
+to allow more complicated scripts or dependent binaries that require:
+
+1. Any number of input data files selected by the user from existing history data
+2. Any number of output data files written to the user's history
+3. Any number of user supplied parameters. These can be passed as command line arguments to the script or the dependency package. Either
+positional or named (argparse) style command line parameter passing can be used.
+
+More complex models can be seen in the Sedtest, Pyrevpos and Pyrevargparse tools illustrating positional and argparse parameter passing.
+
+The most complex demonstration is the Planemo advanced tool tutorial BWA tool. There is one version using a command-override to implement
+exactly the same command structure in the Planemo tutorial. A second version uses a bash script and positional parameters to achieve the same
+result. Some tool builders may find the bash version more familiar and cleaner but the choice is yours.
+
+## Overview
+
+![IHello example ToolFactory tool form](files/hello_toolfactory_form.png?raw=true "Part of the Hello world example ToolFactory tool form")
+
+
+Steps in building a new Galaxy tool are all conducted through Galaxy running in the docker container:
+
+1. Login to the Galaxy running in the container at http://localhost:8080 using an admin account. They are specified in config/galaxy.yml and
+    in the documentation at
+    and the ToolFactory will error out and refuse to run for non-administrative tool builders as a minimal protection from opportunistic hostile use.
+
+2. Start the TF and fill in the form, providing sample inputs and parameter values to suit the Conda package being wrapped.
+
+3. Execute the tool to create a new XML tool wrapper using the sample inputs and parameter settings for the inbuilt tool test. Planemo runs twice.
+    firstly to generate the test outputs and then to perform a proper test. The completed toolshed archive is written to the history
+    together with the planemo test report. Optionally the new tool archive can be uploaded
+    to the toolshed running in the same container (http://localhost:9009) and then installed inside the Galaxy in the container for further testing.
+
+4. If the test fails, rerun the failed history job and correct errors on the tool form before rerunning until everything works correctly.
+
+![How it works](files/TFasIDE.png?raw=true "Overview of the ToolFactory as an Integrated Development Environment")
+
+## Planning and building new Galaxy tool wrappers.
+
+It is best to have all the required planning done to wrap any new script or binary before firing up the TF.
+Conda is the only current dependency manager supported. Before starting, at the very least, the tool builder will need
+to know the required software package name in Conda and the version to use, how the command line for
+the package must be constructed, and there must be sample inputs in the working history for each of the required data inputs
+for the package, together with values for every parameter to suit these sample inputs. These are required on the TF form
+for preparing the inbuilt tool test. That test is run using Planemo, as part of the tool generation process.
+
+A new tool is specified by filling in the usual Galaxy tool form.
+
+The form starts with a new tool name. Most tools will need dependency packages and versions
+for the executable. Only Conda is currently supported.
+
+If a script is needed, it can be pasted into a text box and the interpreter named. Available system executables
+can be used such as bash, or an interpreter such as python, perl or R can be nominated as conda dependencies
+to ensure reproducible analyses.
+
+The tool form will be generated from the input data and the tool builder supplied parameters. The command line for the
+executable is built using positional or argparse (named e.g. --input_file /foo/baz) style
+parameters and is completely dependent on the executable. These can include:
+
+1. Any number of input data sets needed by the executable. Each appears to the tool user on the run form and is included
+on the command line for the executable. The tool builder must supply a small representative sample for each one as
+an input for the automated tool test.
+
+2. Any number of output data sets generated by the package can be added to the command line and will appear in
+the user's history at the end of the job
+
+3. Any number of text or numeric parameters. Each will appear to the tool user on the run form and are included
+on the command line to the executable. The tool builder must supply a suitable representative value for each one as
+the value to be used for the automated tool test.
+
+Once the form is completed, executing the TF will build a new XML tool wrapper
+including a functional test based on the sample settings and data.
+
+If the Planemo test passes, the tool can be optionally uploaded to the local Galaxy used in the image for more testing.
+
+A local toolshed runs inside the container to allow an automated installation, although any toolshed and any accessible
+Galaxy can be specified for this process by editing the default URL and API keys to provide appropriate credentials.
+
+## Generated Tool Dependency management
+
+Conda is used for all dependency management although tools that use system utilities like sed, bash or awk
+may be available on job execution nodes. Sed and friends are available as Conda (conda-forge) dependencies if necessary.
+Versioned Conda dependencies are always baked-in to the tool and will be used for reproducible calculation.
+
+## Requirements
+
+These are all managed automagically. The TF relies on galaxyxml to generate tool xml and uses ephemeris and
+bioblend to load tools to the toolshed and to Galaxy. Planemo is used for testing and runs in a biocontainer currently at
+https://quay.io/fubar2/planemo-biocontainer
+
+## Caveats
+
+This docker image requires privileged mode so exposes potential security risks if hostile tool builders gain access.
+Please, do not run it in any situation where that is a problem - never, ever on a public facing Galaxy server.
+On a laptop or workstation should be fine in a non-hostile environment.
+
+
+## Example generated XML
+
+For the bwa-mem example, a supplied bash script is included as a configfile and so has escaped characters.
+```
+<tool name="bwatest" id="bwatest" version="0.01">
+  <!--Cite: Creating re-usable tools from scripts doi:10.1093/bioinformatics/bts573-->
+  <!--Source in git at: https://github.com/fubar2/toolfactory-->
+  <!--Created by admin@galaxy.org at 30/11/2020 07:12:10 using the Galaxy Tool Factory.-->
+  <description>Planemo advanced tool building sample bwa mem mapper as a ToolFactory demo</description>
+  <requirements>
+    <requirement version="0.7.15" type="package">bwa</requirement>
+    <requirement version="1.3" type="package">samtools</requirement>
+  </requirements>
+  <configfiles>
+    <configfile name="runme"><![CDATA[
+REFFILE=\$1
+FASTQ=\$2
+BAMOUT=\$3
+rm -f "refalias"
+ln -s "\$REFFILE" "refalias"
+bwa index -a is "refalias"
+bwa mem -t "2"  -v 1 "refalias" "\$FASTQ"  > tempsam
+samtools view -Sb tempsam > temporary_bam_file.bam
+samtools sort -o "\$BAMOUT" temporary_bam_file.bam
+
+]]></configfile>
+  </configfiles>
+  <version_command/>
+  <command><![CDATA[bash
+$runme
+$input1
+$input2
+$bam_output]]></command>
+  <inputs>
+    <param optional="false" label="Reference sequence for bwa to map the fastq reads against" help="" format="fasta" multiple="false" type="data" name="input1" argument="input1"/>
+    <param optional="false" label="Reads as fastqsanger to align to the reference sequence" help="" format="fastqsanger" multiple="false" type="data" name="input2" argument="input2"/>
+  </inputs>
+  <outputs>
+    <data name="bam_output" format="bam" label="bam_output" hidden="false"/>
+  </outputs>
+  <tests>
+    <test>
+      <output name="bam_output" value="bam_output_sample" compare="sim_size" format="bam" delta_frac="0.1"/>
+      <param name="input1" value="input1_sample"/>
+      <param name="input2" value="input2_sample"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+
+**What it Does**
+
+Planemo advanced tool building sample bwa mem mapper
+
+Reimagined as a bash script for a ToolFactory demonstration
+
+
+------
+
+Script::
+
+    REFFILE=$1
+    FASTQ=$2
+    BAMOUT=$3
+    rm -f "refalias"
+    ln -s "$REFFILE" "refalias"
+    bwa index -a is "refalias"
+    bwa mem -t "2"  -v 1 "refalias" "$FASTQ"  > tempsam
+    samtools view -Sb tempsam > temporary_bam_file.bam
+    samtools sort -o "$BAMOUT" temporary_bam_file.bam
+
+]]></help>
+</tool>
+
+```
+
+
+
+## More Explanation
+
+The TF is an unusual Galaxy tool, designed to allow a skilled user to make new Galaxy tools.
+It appears in Galaxy just like any other tool but outputs include new Galaxy tools generated
+using instructions provided by the user and the results of Planemo lint and tool testing using
+small sample inputs provided by the TF user. The small samples become tests built in to the new tool.
+
+It offers a familiar Galaxy form driven way to define how the user of the new tool will
+choose input data from their history, and what parameters the new tool user will be able to adjust.
+The TF user must know, or be able to read, enough about the tool to be able to define the details of
+the new Galaxy interface and the ToolFactory offers little guidance on that other than some examples.
+
+Tools always depend on other things. Most tools in Galaxy depend on third party
+scientific packages, so TF tools usually have one or more dependencies. These can be
+scientific packages such as BWA or scripting languages such as Python and are
+managed by Conda. If the new tool relies on a system utility such as bash or awk
+where the importance of version control on reproducibility is low, these can be used without
+Conda management - but remember the potential risks of unmanaged dependencies on computational
+reproducibility.
+
+The TF user can optionally supply a working script where scripting is
+required and the chosen dependency is a scripting language such as Python or a system
+scripting executable such as bash. Whatever the language, the script must correctly parse the command line
+arguments it receives at tool execution, as they are defined by the TF user. The
+text of that script is "baked in" to the new tool and will be executed each time
+the new tool is run. It is highly recommended that scripts and their command lines be developed
+and tested until proven to work before the TF is invoked. Galaxy as a software development
+environment is actually possible, but not recommended being somewhat clumsy and inefficient.
+
+Tools nearly always take one or more data sets from the user's history as input. TF tools
+allow the TF user to define what Galaxy datatypes the tool end user will be able to choose and what
+names or positions will be used to pass them on a command line to the package or script.
+
+Tools often have various parameter settings. The TF allows the TF user to define how each
+parameter will appear on the tool form to the end user, and what names or positions will be
+used to pass them on the command line to the package. At present, parameters are limited to
+simple text and number fields. Pull requests for other kinds of parameters that galaxyxml
+can handle are welcomed.
+
+Best practice Galaxy tools have one or more automated tests. These should use small sample data sets and
+specific parameter settings so when the tool is tested, the outputs can be compared with their expected
+values. The TF will automatically create a test for the new tool. It will use the sample data sets
+chosen by the TF user when they built the new tool.
+
+The TF 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. For this reason, a Docker container is
+available to help manage the associated risks.
+
+## Scripting uses
+
+To use a scripting language to create a new tool, you must first prepared and properly test a script. Use small sample
+data sets for testing. When the script is working correctly, upload the small sample datasets
+into a new history, start configuring a new ToolFactory tool, and paste the script into the script text box on the TF form.
+
+### Outputs
+
+The TF will generate the new tool described on the TF form, and test it
+using planemo. Optionally if a local toolshed is running, it can be used to
+install the new tool back into the generating Galaxy.
+
+A toolshed is built in to the Docker container and configured
+so a tool can be tested, sent to that toolshed, then installed in the Galaxy
+where the TF is running using the default toolshed and Galaxy URL and API keys.
+
+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
+package and/or script that was supplied when it was built will be executed with the input chosen
+from the user's history, together with user supplied parameters. In other words, the tools you generate with the
+TF run just like any other Galaxy tool.
+
+TF generated tools work as normal workflow components.
+
+
+## Limitations
+
+The TF is flexible enough to generate wrappers for many common scientific packages
+but the inbuilt automation will not cope with all possible situations. Users can
+supply overrides for two tool XML segments - tests and command and the BWA
+example in the supplied samples workflow illustrates their use. It does not deal with
+repeated elements or conditional parameters such as allowing a user to choose to see "simple"
+or "advanced" parameters (yet) and there will be plenty of packages it just
+won't cover - but it's a quick and efficient tool for the other 90% of cases. Perfect for
+that bash one liner you need to get that workflow functioning correctly for this
+afternoon's demonstration!
+
+## Installation
+
+The Docker container https://github.com/fubar2/toolfactory-galaxy-docker/blob/main/README.md
+is the best way to use the TF because it is preconfigured
+to automate new tool testing and has a built in local toolshed where each new tool
+is uploaded. If you grab the docker container, it should just work after a restart and you
+can run a workflow to generate all the sample tools. Running the samples and rerunning the ToolFactory
+jobs that generated them allows you to add fields and experiment to see how things work.
+
+It can be installed like any other tool from the Toolshed, but you will need to make some
+configuration changes (TODO write a configuration). 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 in the Tool Maker section. Open it and review the code and select the option to install it.
+
+If not already there please add:
+
+```
+<datatype extension="tgz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" />
+```
+
+to your local config/data_types_conf.xml.
+
+
+## Restricted execution
+
+The tool factory tool itself will ONLY run for admin users -
+people with IDs in config/galaxy.yml "admin_users".
+
+*ONLY admin_users can run this tool*
+
+That doesn't mean it's safe to install on a shared or exposed instance - please don't.
+
+## 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.
+
+## 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
+

--- a/toolfactory/ToolFactory.py	Mon Jun 21 04:18:59 2021 +0000
+++ b/toolfactory/ToolFactory.py	Thu Jul 01 05:52:07 2021 +0000
@@ -851,7 +851,7 @@
     a("--bad_user", default=None)
     a("--help_text", default=None)
     a("--tool_desc", default=None)
-    a("--tool_version", default=None)
+    a("--tool_version", default="0.01")
     a("--citations", default=None)
     a("--command_override", default=None)
     a("--test_override", default=None)

--- a/toolfactory/ToolFactory.xml	Mon Jun 21 04:18:59 2021 +0000
+++ b/toolfactory/ToolFactory.xml	Thu Jul 01 05:52:07 2021 +0000
@@ -143,12 +143,8 @@
         </section>
      </xml>
      <xml name="additparam">
-     <section name="addparam" title="Arguments" help="Executable or script settings passed on the command line other than I/O files" expanded="true">
-        <param name="edit_params" type="hidden" display="radio" label="Make these settings on the generated tool form user editable?"
-             help="If no, users will NOT be able to alter any additional parameters. If yes, these will appear on the tool form as text fields with no validation or sanitizing">
-            <option value="yes" selected="true">Yes, allow user to edit all additional parameters on the generated tool form</option>
-            <option value="no">No - use the fixed values for all additional parameters - no user editing</option>
-        </param>
+     <section name="addparam" title="Executable or script settings passed on the command line other than I/O files" expanded="true">
+        <param name="edit_params" type="hidden" />
         <repeat name="additional_parameters" title="User supplied parameters" min="0"
              help="Settings for the user to adjust. Passed to the executable on the command line. See examples below to see how these can be parsed by scripts in various languages">
           <param name="param_name" type="text" value="" label="Choose the name for this parameter - MUST not be blank!">
@@ -363,7 +359,6 @@
             <expand macro="additparam" />
         </when>
         <when value="0">
-             <expand macro="io"/>
         </when>
     </conditional>
     </section>
@@ -412,7 +407,7 @@
     <param name="input_files" value="input1_sample" />
     <param name="input_CL" value="1" />
     <param name="input_formats" value="txt" />
-    <param name="input_label" value="input" />
+    <param name="input_label" value="input" />rm
     <param name="input_help" value="help" />
     <param name="tool_name" value="pyrevpos" />
     <param name="parampass" value="positional" />

--- a/toolfactory/ToolFactoryDemosApril30.ga	Mon Jun 21 04:18:59 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,965 +0,0 @@
-{
-    "a_galaxy_workflow": "true",
-    "annotation": "",
-    "format-version": "0.1",
-    "name": "ToolFactory - make, test and install demonstration tools",
-    "steps": {
-        "0": {
-            "annotation": "",
-            "content_id": "rgtf2",
-            "errors": null,
-            "id": 0,
-            "input_connections": {},
-            "inputs": [],
-            "label": null,
-            "name": "toolfactory",
-            "outputs": [
-                {
-                    "name": "new_tool",
-                    "type": "toolshed.gz"
-                }
-            ],
-            "position": {
-                "bottom": -152.39999389648438,
-                "height": 102.60000610351562,
-                "left": 252.5,
-                "right": 452.5,
-                "top": -255,
-                "width": 200,
-                "x": 252.5,
-                "y": -255
-            },
-            "post_job_actions": {},
-            "tool_id": "rgtf2",
-            "tool_state": "{\"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"dbb99db2a98811ebbc9e0242ac1b0004\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_prefix\": \"\", \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"bash\", \"dynScript\": \"echo \\\"Hello $1\\\"\"}}, \"help_text\": \"**What it Does**\", \"install\": \"false\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"Hello_output\", \"history_format\": \"txt\", \"history_CL\": \"STDOUT\", \"history_test\": \"diff:0\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": [{\"__index__\": 0, \"param_name\": \"say_hello_to\", \"ap_type\": {\"param_type\": \"text\", \"__current_case__\": 0, \"param_value\": \"\"}, \"param_label\": \"Say hello to\", \"param_help\": \"\", \"param_CL\": \"1\", \"param_CLprefixed\": \"\", \"param_repeat\": \"false\"}]}}}, \"make\": {\"makeMode\": {\"__current_case__\": 1, \"citations\": [], \"galaxy_apikey\": \"fakekey\", \"galaxy_url\": \"http://localhost:8080\", \"help_text\": \"**What it Does**\\nToolFactory demonstration - hello world in Galaxy\", \"make_Tool\": \"gentest\", \"tool_desc\": \"Says hello\", \"tool_version\": \"0.01\", \"toolshed_apikey\": \"fakekey\", \"toolshed_url\": \"http://localhost:9009\"}}, \"run_test\": \"true\", \"tool_desc\": \"\", \"tool_name\": \"hello_toolshed\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2.00",
-            "type": "tool",
-            "uuid": "f07cf7c8-4a96-4c4f-bd7b-d43c30642369",
-            "workflow_outputs": [
-                {
-                    "label": null,
-                    "output_name": "new_tool",
-                    "uuid": "5e1e49e0-ed56-4c7a-95fe-2f66aa4d7165"
-                }
-            ]
-        },
-        "1": {
-            "annotation": "",
-            "content_id": null,
-            "errors": null,
-            "id": 1,
-            "input_connections": {},
-            "inputs": [
-                {
-                    "description": "",
-                    "name": "bwa-mem-fastq1.fq"
-                }
-            ],
-            "label": "bwa-mem-fastq1.fq",
-            "name": "Input dataset",
-            "outputs": [],
-            "position": {
-                "bottom": 353.1999969482422,
-                "height": 82.19999694824219,
-                "left": 252.5,
-                "right": 452.5,
-                "top": 271,
-                "width": 200,
-                "x": 252.5,
-                "y": 271
-            },
-            "tool_id": null,
-            "tool_state": "{\"optional\": false}",
-            "tool_version": null,
-            "type": "data_input",
-            "uuid": "e1c43d57-ee0e-42ea-aed7-d86c595d06e7",
-            "workflow_outputs": [
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-                    "label": null,
-                    "output_name": "output",
-                    "uuid": "ecd799ad-b7be-4b58-87ea-050884620d99"
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-            "id": 2,
-            "input_connections": {},
-            "inputs": [
-                {
-                    "description": "",
-                    "name": "bwa-mem-mt-genome.fa"
-                }
-            ],
-            "label": "bwa-mem-mt-genome.fa",
-            "name": "Input dataset",
-            "outputs": [],
-            "position": {
-                "bottom": 473.1999969482422,
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-                "left": 252.5,
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-                "top": 391,
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-            "uuid": "98ae8bb5-cd5c-4330-b0cc-4d2252b0eee1",
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-                    "uuid": "c0b94cf6-886f-4260-9e63-a2e57435a628"
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-        "3": {
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-            "id": 3,
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-            "inputs": [
-                {
-                    "description": "",
-                    "name": "hello_toolshed_toolshed.gz"
-                }
-            ],
-            "label": "hello_toolshed_toolshed.gz",
-            "name": "Input dataset",
-            "outputs": [],
-            "position": {
-                "bottom": -333.8000030517578,
-                "height": 82.19999694824219,
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-            "tool_state": "{\"optional\": false}",
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-        "4": {
-            "annotation": "",
-            "content_id": "rgtf2",
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-            "id": 4,
-            "input_connections": {},
-            "inputs": [],
-            "label": null,
-            "name": "toolfactory",
-            "outputs": [
-                {
-                    "name": "new_tool",
-                    "type": "toolshed.gz"
-                }
-            ],
-            "position": {
-                "bottom": -313.3999938964844,
-                "height": 102.60000610351562,
-                "left": 530.5,
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-            "post_job_actions": {},
-            "tool_id": "rgtf2",
-            "tool_state": "{\"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"dbb99db2a98811ebbc9e0242ac1b0004\", \"chromInfo\": \"/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"citations\": [], \"cl_prefix\": \"\", \"cl_suffix\": \"\", \"cover\": {\"commover\": \"no\", \"__current_case__\": 0, \"command_override\": \"\", \"test_override\": \"\"}, \"deps\": {\"packages\": \"planemo\", \"usescript\": {\"choosescript\": \"yes\", \"__current_case__\": 1, \"scriptrunner\": \"bash\", \"dynScript\": \"cp $1 foo.tar.gz\\ntar -xvf foo.tar.gz\\nTOOLNAME=`find . -name \\\"*.xml\\\"`\\necho \\\"TOOLNAME = $TOOLNAME\\\"\\nplanemo test  --test_output $2 $TOOLNAME\"}}, \"help_text\": \"**What it Does**\", \"install\": \"false\", \"io_param\": {\"ppass\": {\"parampass\": \"positional\", \"__current_case__\": 1, \"io\": {\"history_inputs\": [{\"__index__\": 0, \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"input_formats\": [\"tgz\"], \"input_label\": \"ToolFactory toolshed archive from the history to test\", \"input_help\": \"\", \"input_CL\": \"1\", \"input_repeat\": \"false\"}], \"history_outputs\": [{\"__index__\": 0, \"history_name\": \"planemo_test_output\", \"history_format\": \"txt\", \"history_CL\": \"2\", \"history_test\": \"sim_size:0.05\"}], \"collection_outputs\": []}, \"addparam\": {\"edit_params\": \"yes\", \"additional_parameters\": []}}}, \"make\": {\"makeMode\": {\"__current_case__\": 1, \"citations\": [], \"galaxy_apikey\": \"\", \"galaxy_url\": \"\", \"help_text\": \"**What it Does**\\n\\nRuns planemo test on a ToolFactory or other toolshed archive\", \"make_Tool\": \"gentest\", \"tool_desc\": \"Tests a ToolFactory tool\", \"tool_version\": \"0.01\", \"toolshed_apikey\": \"\", \"toolshed_url\": \"\"}}, \"run_test\": \"true\", \"tool_desc\": \"\", \"tool_name\": \"planemo_test\", \"tool_version\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2.00",
-            "type": "tool",
-            "uuid": "2d826252-a3fc-4e99-8791-2908926cda10",
-            "workflow_outputs": [
-                {
-                    "label": null,
-                    "output_name": "new_tool",
-                    "uuid": "659cabcf-e7db-4b61-8e3c-097a1d25c336"
-                }
-            ]
-        }
-    },
-    "tags": [],
-    "uuid": "308d4b95-f04f-49b0-8674-f0ddf0587850",
-    "version": 1
-}

--- a/toolfactory/test-data/output2_sample	Mon Jun 21 04:18:59 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,165 +0,0 @@
-*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

--- a/toolfactory/test-data/pyrevpos.python	Mon Jun 21 04:18:59 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-# 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() 
-

Binary file toolfactory/test-data/pyrevpos_not_tested.toolshed_sample has changed

--- a/toolfactory/test-data/test1_log.txt	Mon Jun 21 04:18:59 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-## 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