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scriptrunner: minor doc improvement #16

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scriptrunner: minor doc improvement #16

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90108c8
scriptrunner: minor doc improvement
bernt-matthias Dec 4, 2023
afb8641
tee stdout
bernt-matthias Feb 27, 2024
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66 changes: 63 additions & 3 deletions tools/scripting/general.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="singularity_scriptrunner" name="scriptrunner" version="0.1" profile="22.05">
<tool id="singularity_scriptrunner" name="scriptrunner" version="0.1.1" profile="22.05">
<description>singularity</description>
<creator>
<person givenName="Matthias" familyName="Bernt" email="m.bernt@ufz.de" />
Expand Down Expand Up @@ -44,6 +44,7 @@
'$p.type_cond.param'
#end if
#end for
| tee '$log'
]]></command>
<configfiles>
<configfile name="script">$code</configfile>
Expand Down Expand Up @@ -73,7 +74,7 @@
</param>
<when value="data">
<param name="param" type="data" format="data" label="Dataset"/>
<param name="filename" type="text" label="File name" help="Set if you want to access the data set with a specific file name. Only alphanumeric characters, dash and underscore are allowed (all other characters are replaced by an undercore). Default is Galaxy's data set name.">
<param name="filename" type="text" label="File name" help="Set if you want to access the data set with a specific file name (default is access via argument vector, see help). Data will be accessible at inputs/FILENAME, where FILENAME is the chosen file name. Only alphanumeric characters, dash and underscore are allowed (all other characters are replaced by an undercore). Default is Galaxy's data set name.">
<sanitizer invalid_char="_">
<valid initial="string.ascii_letters,string.digits">
<add value="_" />
Expand All @@ -97,7 +98,8 @@
</param>
</inputs>
<outputs>
<collection name="output" type="list" label="Outputs">
<data name="log" format="txt" label="${tool.name} on ${on_string}: Log"/>
<collection name="output" type="list" label="${tool.name} on ${on_string}: Outputs">
<discover_datasets pattern="__designation_and_ext__"/>
</collection>
</outputs>
Expand All @@ -122,6 +124,11 @@
</assert_contents>
</element>
</output_collection>
<output name="log">
<assert_contents>
<has_n_lines n="0"/>
</assert_contents>
</output>
<!-- but the data table this should use singularity and not use additional parameters to it (\-\-cleanenv) -->
<assert_command>
<has_text text="singularity"/>
Expand All @@ -146,6 +153,11 @@
</assert_contents>
</element>
</output_collection>
<output name="log">
<assert_contents>
<has_n_lines n="0"/>
</assert_contents>
</output>
<assert_stdout>
<has_line line="plotted inputs/custom_name.tsv"/>
</assert_stdout>
Expand All @@ -166,6 +178,11 @@
</conditional>
</repeat>
<param name="code" value='import sys; import os; import pandas as pd; df = pd.read_hdf(sys.argv[1]); df.to_csv("data.csv", index=False, sep=",");'/>
<output name="log">
<assert_contents>
<has_n_lines n="0"/>
</assert_contents>
</output>
<output_collection name="output" type="list" count="1">
<element name="data" ftype="csv">
<assert_contents>
Expand Down Expand Up @@ -202,6 +219,12 @@
</assert_contents>
</element>
</output_collection>
<output name="log">
<assert_contents>
<has_n_lines n="1"/>
<has_line line="some value"/>
</assert_contents>
</output>
<assert_stdout>
<has_line line='some value'/>
</assert_stdout>
Expand All @@ -226,6 +249,12 @@
</assert_contents>
</element>
</output_collection>
<output name="log">
<assert_contents>
<has_n_lines n="1"/>
<has_line line="some value"/>
</assert_contents>
</output>
<!-- but the data table this should use apptainer and not use any additional parameters to it -->
<assert_command>
<has_text text="apptainer"/>
Expand All @@ -250,6 +279,12 @@
</assert_contents>
</element>
</output_collection>
<output name="log">
<assert_contents>
<has_n_lines n="1"/>
<has_line line='[1] "plotted inputs/custom_name.tsv"'/>
</assert_contents>
</output>
<assert_stdout>
<has_line line='[1] "plotted inputs/custom_name.tsv"'/>
</assert_stdout>
Expand All @@ -275,6 +310,12 @@
</conditional>
</repeat>
<param name="code" value='args = commandArgs(trailingOnly = TRUE); data = readRDS(args[1]); write.csv(data, "data.csv", row.names=FALSE)'/>
<output name="log">
<assert_contents>
<has_n_lines n="1"/>
<has_line line='[1] "plotted inputs/custom_name.tsv"'/>
</assert_contents>
</output>
<output_collection name="output" type="list" count="1">
<element name="data" ftype="csv">
<assert_contents>
Expand Down Expand Up @@ -311,6 +352,19 @@
</assert_contents>
</element>
</output_collection>
<output name="log">
<assert_contents>
<has_n_lines n="1"/>
<has_line line='[1] "plotted inputs/custom_name.tsv"'/>
</assert_contents>
</output>

<output name="log">
<assert_contents>
<has_n_lines n="1"/>
<has_line line='[1] "plotted inputs/custom_name.tsv"'/>
</assert_contents>
</output>
<assert_stdout>
<has_line line='[1] "some value"'/>
</assert_stdout>
Expand All @@ -335,6 +389,12 @@
</assert_contents>
</element>
</output_collection>
<output name="log">
<assert_contents>
<has_n_lines n="1"/>
<has_line line='[1] "plotted inputs/custom_name.tsv"'/>
</assert_contents>
</output>
</test>

<!-- check that we can turn off networking -->
Expand Down
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