annotate general.xml @ 2:2eb0532a911c draft default tip

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/ commit 8c309a4891e29a0fd273f9edc37292e1f3965317

<tool id="singularity_scriptrunner" name="scriptrunner" version="0.2" profile="22.05">
    <description>singularity</description>
    <creator>
        <person givenName="Matthias" familyName="Bernt" email="[e-mail]" />
        <organization name="Helmholtz Centre for Environmental Research - UFZ" url="https://www.ufz.de/"/>
    </creator>
    <command detect_errors="aggressive"><![CDATA[
        #import re

        ## cp script to JWD
        mkdir script &&
        cp '$script' script/script &&

        mkdir inputs &&
        #for $p in $parameters
            #if $p.type_cond.type_sel == "data"
                #if $p.type_cond.filename != ''
                    #set fname = $p.type_cond.filename
                #else
                    #set fname=re.sub('[^\s\w\.]', '_', str($p.type_cond.param.element_identifier)) + "." + $p.type_cond.param.ext
                #end if
                ln -s '$p.type_cond.param' inputs/'$fname' &&
            #end if
        #end for

        $image.fields.container_type
        exec
            ## --cpus 1 # disabled because rootless cgroups requires cgroups v2
            ## --memory "\$((1024 * \${GALAY_MEMORY_MB:-8192}))" # not needed on EVE
            ## bind Galaxy's file dir, otherwise we need to copy input file to JWD
            --bind '$__app__.config.file_path:$__app__.config.file_path'
            $image.fields.container_params
        '$image.fields.image'
        $image.fields.interpreter 'script/script'
        #for $p in $parameters
            #if $p.type_cond.type_sel == "data"
                #if $p.type_cond.filename != ''
                    #set fname = $p.type_cond.filename
                #else
                    #set fname=re.sub('[^\s\w\.]', '_', str($p.type_cond.param.element_identifier)) + "." + $p.type_cond.param.ext
                #end if
                inputs/'$fname'
            #else
                '$p.type_cond.param'
            #end if
        #end for
    ]]></command>
    <configfiles>
        <configfile name="script">$code</configfile>
    </configfiles>
    <inputs>
        <param name="image" type="select" label="Image" >
            <options from_data_table="scripting_images"/>
            <validator type="no_options" message="No image is available. Contact you Galaxy administrator." />
        </param>
        <repeat name="parameters" title="Parameters" min="0" default="1" help="Supply parameters">
            <conditional name="type_cond">
                <param name="type_sel" type="select" label="Parameter type">
                    <option value="data">Dataset</option>
                    <option value="text">Text</option>
                    <!-- Not sure if int/float make sense .. can they be connected to text in WFs? -->
                </param>
                <when value="data">
                    <param name="param" type="data" format="data" label="Dataset"/>
                    <param name="filename" type="text" label="File name" help="Set if you want to access the data set with a specific file name. Only alphanumeric characters, dash and underscore are allowed (all other characters are replaced by an undercore). Default is Galaxy's data set name.">
                        <sanitizer invalid_char="_">
                            <valid initial="string.ascii_letters,string.digits">
                                <add value="_" />
                                <add value="-" />
                                <add value="." />
                            </valid>
                        </sanitizer> 
                        <!-- file names must not start with dash -->
                        <validator type="regex" negate="true" message="Filenames must not start with a dash">^[-].*$</validator>
                    </param>
                </when>
                <when value="text">
                    <param name="param" type="text" label="Text parameter" help=""/>
                </when>
            </conditional>
        </repeat>
        <param name="code" type="text" area="true" label="Script to execute" help="">
            <sanitizer>
                <valid initial="string.printable"/>
            </sanitizer>
        </param>
    </inputs>
    <outputs>
        <collection name="output" type="list" label="Outputs">
            <discover_datasets pattern="__designation_and_ext__"/>
        </collection>
    </outputs>
    <tests>
        <!-- read tsv write csv -->
        <test>
            <param name="image" value="python_python"/>
            <repeat name="parameters">
                <conditional name="type_cond">
                    <param name="type_sel" value="data"/>
                    <param name="param" value="test.tsv" ftype="tabular"/>
                </conditional>
            </repeat>
            <param name="code" value='import sys, subprocess; subprocess.check_call([sys.executable, "-m", "pip", "install", "pandas", "matplotlib"]); import pandas as pd; df = pd.read_csv(sys.argv[1], sep="\t"); df.to_csv("data.csv", index=False, sep=",");'/>
            <output_collection name="output" type="list" count="1">
                <element name="data" ftype="csv">
                    <assert_contents>
                        <has_line line="1,2" />
                        <has_n_lines n="3"/>
                        <has_n_columns n="2" sep=","/>
                    </assert_contents>
                </element>
            </output_collection>
            <!-- but the data table this should use singularity and not use additional parameters to it (\-\-cleanenv) -->
            <assert_command>
                <has_text text="singularity"/>
                <has_text text="--cleanenv"/>
            </assert_command>
        </test>
        <!-- plot w matplotlib -->
        <test>
            <param name="image" value="python_python"/>
            <repeat name="parameters">
                <conditional name="type_cond">
                    <param name="param" value="test.tsv" ftype="tabular"/>
                    <param name="filename" value="custom_name.tsv"/>
                </conditional>
            </repeat>
            <param name="code" value='import sys, subprocess; subprocess.check_call([sys.executable, "-m", "pip", "install", "pandas", "matplotlib"]); import pandas as pd; from matplotlib.backends.backend_pdf import PdfPages;  df = pd.read_csv(sys.argv[1], sep="\t"); fh = PdfPages("points.pdf"); plt = df.plot(); fh.savefig(); fh.close(); print(f"plotted {sys.argv[1]}")'/>
            <output_collection name="output" type="list" count="1">
                <element name="points" ftype="pdf">
                    <assert_contents>
                        <has_text text="PDF" />
                    </assert_contents>
                </element>
            </output_collection>
            <assert_stdout>
                <has_line line="plotted inputs/custom_name.tsv"/>
            </assert_stdout>
        </test>
        <!-- install libraries ("forbidden") -->
        <test expect_failure="true">
            <param name="image" value="python_python_noinstall"/>
            <repeat name="parameters">
                <!-- mocking test here .. can't leave the repeat empty (in the test)
                     since Galaxy will expect the data parameter anyway 
                     https://github.com/galaxyproject/galaxy/pull/19472 -->
                <conditional name="type_cond">
                    <param name="type_sel" value="text"/>
                </conditional>
            </repeat>
            <param name="code" value='import pip; pip.main(["install", "biopython"]); import Bio'/>
        </test>
        <!-- read binary files (eg feather)  -->
        <test>
            <param name="image" value="python_python"/>
            <repeat name="parameters">
                <conditional name="type_cond">
                    <param name="param" value="test.h5" ftype="h5"/>
                </conditional>
            </repeat>
            <param name="code" value='import sys, subprocess; subprocess.check_call([sys.executable, "-m", "pip", "install", "pandas", "matplotlib", "tables"]); import os; import pandas as pd; df = pd.read_hdf(sys.argv[1]); df.to_csv("data.csv", index=False, sep=",");'/>
            <output_collection name="output" type="list" count="1">
                <element name="data" ftype="csv">
                    <assert_contents>
                        <has_line line="1,2" />
                        <has_n_lines n="3"/>
                        <has_n_columns n="2" sep=","/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <!-- parameters -->
        <test>
            <param name="image" value="python_python"/>
            <repeat name="parameters">
                <conditional name="type_cond">
                    <param name="type_sel" value="text"/>
                    <param name="param" value="filename.csv"/>
                </conditional>
            </repeat>
            <repeat name="parameters">
                <conditional name="type_cond">
                    <param name="type_sel" value="text"/>
                    <param name="param" value="some value"/>
                </conditional>
            </repeat>
            <param name="code" value='import sys, subprocess; subprocess.check_call([sys.executable, "-m", "pip", "install", "pandas", "matplotlib"]);  fh = open(sys.argv[1], "w"); fh.write("Hello,world\n"); fh.write("Bye,world\n"); fh.close(); print(sys.argv[2]);'/>
            <output_collection name="output" type="list" count="1">
                <element name="filename" ftype="csv">
                    <assert_contents>
                        <has_line line="Hello,world"/>
                        <has_n_lines n="2"/>
                        <has_n_columns n="2" sep=","/>
                    </assert_contents>
                </element>
            </output_collection>
            <assert_stdout>
                <has_line line='some value'/>
            </assert_stdout>
        </test>

        <!-- read tsv write csv -->
        <test>
            <param name="image" value="r_rocker_tidyverse"/>
            <repeat name="parameters">
                <conditional name="type_cond">
                    <param name="param" value="test.tsv" ftype="tabular"/>
                </conditional>
            </repeat>
            <param name="code" value='args = commandArgs(trailingOnly = TRUE); install.packages("data.table", lib=Sys.getenv("R_LIBS_USER")); library(data.table); data = read.delim(args[1]); write.csv(data, "data.csv", row.names=FALSE)'/>
            <output_collection name="output" type="list" count="1">
                <element name="data" ftype="csv">
                    <assert_contents>
                        <has_line line="1,2" />
                        <has_n_lines n="3"/>
                        <has_n_columns n="2" sep=","/>
                    </assert_contents>
                </element>
            </output_collection>
            <!-- but the data table this should use apptainer and not use any additional parameters to it -->
            <assert_command>
                <has_text_matching expression="apptainer|singularity"/>
                <has_text text="--cleanenv"/>
            </assert_command>
        </test>
        <!-- use a tidyverse library -->
        <test>
            <param name="image" value="r_rocker_tidyverse"/>
            <repeat name="parameters">
                <conditional name="type_cond">
                    <param name="param" value="test.tsv" ftype="tabular"/>
                    <param name="filename" value="custom_name.tsv"/>
                </conditional>
            </repeat>
            <param name="code" value='library(ggplot2); args = commandArgs(trailingOnly = TRUE); data = read.delim(args[1]); pdf("points.pdf"); ggplot(data, aes(x=A, y=B)) + geom_point(); dev.off(); print(paste("plotted", args[1]))'/>
            <output_collection name="output" type="list" count="1">
                <element name="points" ftype="pdf">
                    <assert_contents>
                        <has_text text="PDF" />
                    </assert_contents>
                </element>
            </output_collection>
            <assert_stdout>
                <has_line line='[1] "plotted inputs/custom_name.tsv"'/>
            </assert_stdout>
        </test>
        <!-- install libraries fails -->
        <test expect_failure="true">
            <param name="image" value="r_rocker_tidyverse"/>
            <repeat name="parameters">
                <!-- mocking test here .. can't leave the repeat empty (in the test)
                     since Galaxy will expect the data parameter anyway 
                     https://github.com/galaxyproject/galaxy/pull/19472 -->
                <conditional name="type_cond">
                    <param name="type_sel" value="text"/>
                </conditional>
            </repeat>
            <param name="code" value='install.packages("maybe"); library(maybe); print("success")'/>
        </test>
        <test expect_failure="true">
            <param name="image" value="r_rocker_tidyverse"/>
            <repeat name="parameters">
                <!-- mocking test here .. can't leave the repeat empty (in the test)
                     since Galaxy will expect the data parameter anyway 
                     https://github.com/galaxyproject/galaxy/pull/19472 -->
                <conditional name="type_cond">
                    <param name="type_sel" value="text"/>
                </conditional>
            </repeat>
            <param name="code" value='install.packages("BiocManager"); BiocManager::install("multtest"); print("success")'/>
        </test>
        <!-- read binary files (eg rds) -->
        <test>
            <param name="image" value="r_rocker_tidyverse"/>
            <repeat name="parameters">
                <conditional name="type_cond">
                    <param name="param" value="test.rds" ftype="rds"/>
                </conditional>
            </repeat>
            <param name="code" value='args = commandArgs(trailingOnly = TRUE); data = readRDS(args[1]); write.csv(data, "data.csv", row.names=FALSE)'/>
            <output_collection name="output" type="list" count="1">
                <element name="data" ftype="csv">
                    <assert_contents>
                        <has_line line="1,2" />
                        <has_n_lines n="3"/>
                        <has_n_columns n="2" sep=","/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <!-- optional input and parameters -->
        <test>
            <param name="image" value="r_rocker_tidyverse"/>
            <repeat name="parameters">
                <conditional name="type_cond"> 
                    <param name="type_sel" value="text"/>
                    <param name="param" value="filename.csv"/>
                </conditional>
            </repeat>
            <repeat name="parameters">
                <conditional name="type_cond"> 
                    <param name="type_sel" value="text"/>
                    <param name="param" value="some value"/>
                </conditional>
            </repeat>
            <param name="code" value='args = commandArgs(trailingOnly = TRUE); fileConn = file(args[1]); writeLines(c("Hello,world","Bye,world"), fileConn); close(fileConn); print(args[2]);'/>
            <output_collection name="output" type="list" count="1">
                <element name="filename" ftype="csv">
                    <assert_contents>
                        <has_line line="Hello,world"/>
                        <has_n_lines n="2"/>
                        <has_n_columns n="2" sep=","/>
                    </assert_contents>
                </element>
            </output_collection>
            <assert_stdout>
                <has_line line='[1] "some value"'/>
            </assert_stdout>
        </test>

        <!-- some tests with bash-->
        <test>
            <param name="image" value="bash_python"/>
            <repeat name="parameters">
                <conditional name="type_cond">
                    <param name="param" value="test.tsv" ftype="tabular"/>
                </conditional>
            </repeat>
            <param name="code" value="sed -e 's/\t/,/' $1 > data.csv"/>
            <output_collection name="output" type="list" count="1">
                <element name="data" ftype="csv">
                    <assert_contents>
                        <has_line line="1,2" />
                        <has_n_lines n="3"/>
                        <has_n_columns n="2" sep=","/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>

        <!-- check that we can turn off networking -->
        <test expect_failure="false">
            <param name="image" value="bash_rocker_tidyverse"/>
            <repeat name="parameters">
                <conditional name="type_cond">
                    <param name="param" value="test.tsv" ftype="tabular"/>
                </conditional>
            </repeat>
            <param name="code" value="wget https://www.galaxyproject.org"/>
        </test>
    </tests>
    <help><![CDATA[
**Warning**

.. class:: warningmark

**Make sure that you know what you are doing. When used wrong the tool may lead to
data loss of files that you can write to.**

.. class:: warningmark

This tool is only intended to serve for single-use, ad-hoc exploratory analysis
of data sets with small scripts. This is because the tool has a limited 
reusuability (in particular on other Galaxy servers).

.. class:: warningmark

If you use this tool repeatedly with the same script and/or have the impression
that other Galaxy users could profit from this script then contact your local
Galaxy administrator or the Galaxy community, e.g. at https://github.com/galaxyproject/tools-iuc/,
and ask if your script can be turned into a proper Galaxy tool.
One of the main advantages of a proper Galaxy tool is that they are tested and
maintained. Furthermore the whole Galaxy community may profit.

**What it does**

Executes an interpreted script (in a container). The available scripting
languages (e.g. python, R, bash, etc) and containers are configured by the
Galaxy administrator.

An arbitrary number of data or text parameters can be given to the script.
Data parameters are by default named like the datasets name and the datatype
is used as extension. This can be overwritten with the filename parameter
for the corresponding dataset.

**Inputs**

A python script can access data set parameters via the ``sys.argv`` list
where the i-th parameter corresponds to the i-th list element (counting from 1).
A tab delimited file, for instance, can be read with ``pandas`` as follows:

::

    import sys
    import pandas as pd
    df = pd.read_csv(sys.argv[1], sep="\t")

In an R script the list obtained by ``args <- commandArgs(trailingOnly = TRUE);``
contains (again the i-th list element contains the i-th parameter, starting from 1).
Reading a tab separated file in R could be done as follows:
            
::

    args <- commandArgs(trailingOnly = TRUE);
    first_arg <- file(args[1])
    df <- read.delim(args[1]);

**Outputs**

Output datasets are read from the current working directory and put into a
single collection.  The collection elements will be named as the file names
(without the extension). The file extension determines the datatype of the
datasets (or Galaxy will try to autodetect the data type).

**Custom 3rd party packages or libraries**

Installation of 3rd party software might work depending on the container
and the 3rd party software. For python and R the following can work. In case
of problems contact your Galaxy administrator.

To install two packages ``PACKAGE1`` and ``PACKAGE2`` in python:

::
    import sys, subprocess
    subprocess.check_call([sys.executable, "-m", "pip", "install", "PACKAGE1", "PACKAGE2"]);

For R scripts the following will install two libraries ``LIBRARY1`` and ``LIBRARY2``:

::
    install.packages(c("LIBRARY1", "LIBRARY2"), lib=Sys.getenv("R_LIBS_USER"));

    ]]></help>
</tool>