<tool id="ms_to_peakforest_it" name="MS To PeakForest IT" tool_type="interactive" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <description>
        adds you MS spectrum to peakforest.
    </description>
    <macros>
        <token name="@VERSION_SUFFIX@">0</token>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="3.10">python</requirement>
        <requirement type="package">pyyaml</requirement>
    </requirements>
    <entry_points>
        <entry_point name="MS to PeakForest, with ${','.join(str(i.name) for i in $input)}" requires_domain="True">
            <port>8000</port>
            <url>/</url>
        </entry_point>
    </entry_points>
    <version_command>
<![CDATA[
python3 '$__tool_directory__/server.py' --version | head -n 1
]]>
    </version_command>
    <command>
@MS2PF_COMMON_CMD@
    </command>
    <inputs>
        <expand macro="ms2pf_inputs" />
    </inputs>
    <outputs>
        <data name="ms2pfout" format="txt"
            label="${tool.name} on ${','.join(i.name for i in $input)}"
        />
        <data name="json_output" format="json"
            label="JSON ${tool.name} on ${','.join(i.name for i in $input)}.json"
        >
            <filter>do_output_json</filter>
        </data>
    </outputs>
    <tests>
    </tests>
    <help>
<![CDATA[
.. class:: infomark

**Authors** Lain Pavot (lain.pavot@inrae.fr)

.. class:: infomark

---------------------------------------------------

==============
MS2 validation
==============

-----------
Description
-----------


-----------------
Workflow position
-----------------

--------------
Upstream tools
--------------

+-------------------------+-----------------+--------+------------+
| Name                    |  output file    | format |  parameter |
+=========================+=================+========+============+
| ms2snoop                |       tsv       |   TSV  |    NA      |
+-------------------------+-----------------+--------+------------+
| abinitfragnot           |       tsv       |   TSV  |    NA      |
+-------------------------+-----------------+--------+------------+

----------------
Downstream tools
----------------

+-------------------------+-----------------+--------+------------+
| Name                    |  output file    | format |  parameter |
+=========================+=================+========+============+
| NA                      |       NA        |   NA   |    NA      |
+-------------------------+-----------------+--------+------------+


-----------
Input files
-----------

+----------------------------------------------+------------+
| Parameter : num + label                      |   Format   |
+===========================+==================+============+
| Output from ms2snoop or fragnot              |   TSV,CSV  |
+----------------------------------------------+------------+

----------
Parameters
----------

input
  | The file to process. Should contain spectra with mz, intensities and
  annotations

method
  | The method parameter tells which method was used. The value will
    be the default value in the peakforest form.

peakforest-url
  | The peakforest-url parameter tells which instance of peakforest to
    interact with

scan_type
  | The scan_type parameter which kind of scan was used. The value will
    be the default value in the peakforest form.

polarity
  | The polarity parameter which polarity was used. The value will
    be the default value in the peakforest form.

name
  | The name parameter provides names each spectra.


------------
Output files
------------

There is not output file. When you run this tool, keep waiting until the
« click here to display » link appears.

Click on the link to display peakforest form.

--------------
Changelog/News
--------------

1.0.0
  | First version, published on the toolshed.

]]>
    </help>
</tool>