Mercurial > repos > ximgchess > chap_test_20230411
changeset 84:1e02b5c4abdf draft
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 795063bb3aaabb2f0ad99135bc2102217bdf91b3-dirty
| author | ximgchess |
|---|---|
| date | Mon, 15 May 2023 19:15:16 +0000 |
| parents | 9b6e931e0de0 |
| children | d58f090c7073 |
| files | tomo/.tomo_reduce.bu.swp tomo/tomo_reduce.bu tomo/tomo_reduce.xml tomo/tomo_reduce_old.xml |
| diffstat | 4 files changed, 94 insertions(+), 95 deletions(-) [+] |
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--- a/tomo/tomo_reduce.bu Tue May 02 15:07:28 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,94 +0,0 @@ -<tool id="CHAP_tomo_reduce" name="Tomo Reduce" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@"> - <description>Reduce tomography images</description> - <macros> - <import>tomo_macros.xml</import> - </macros> - <expand macro="requirements"/> - <command detect_errors="exit_code"> - <![CDATA[ - mkdir tomo_reduce_plots; - $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' && - #if str($map.type_selector) == "yaml" - cp $input_file map.yaml && - cat $__tool_directory__/$map.detector.type_selector $tool_config > reduce.yaml && - #else - cp $input_file setup.nex && - cp $tool_config reduce.yaml && - #end if - CHAP --config - #if str($map.type_selector) == "yaml" - $__tool_directory__/pipeline_reduce_yaml.yaml - #else - $__tool_directory__/pipeline_reduce_nexus.yaml - #end if - ]]> - </command> - <configfiles> - <configfile name="tool_config"> - <![CDATA[#slurp -#echo 'img_x_bounds:' # -#if str($img_x_bounds.type_selector) == "full_range" -#echo '- -1' # -#echo '- -1' # -#else -#echo '- ' + str($img_x_bounds.low) # -#echo '- ' + str($img_x_bounds.upp) # -#end if - ]]> - </configfile> - </configfiles> - <inputs> - <conditional name="map"> - <param name="type_selector" type="select" display="radio" label="Choose map file type"> - <option value="yaml">YAML</option> - <option value="nexus">NeXus</option> - </param> - <when value="yaml"> - <param name="input_file" type="data" format="yaml" optional="false" label="Map config file"/> - <conditional name="detector"> - <param name="type_selector" type="select" display="radio" label="Choose detector prefix"> - <option value="andor2.yaml">andor2</option> - <option value="manta.yaml">manta</option> - <option value="retiga.yaml">retiga</option> - </param> - <when value="andor2"/> - <when value="manta"/> - <when value="retiga"/> - </conditional> - </when> - <when value="nexus"> - <param name="input_file" type="data" format="nex" optional="false" label="Tomography setup file"/> - </when> - </conditional> - <conditional name="img_x_bounds"> - <param name="type_selector" type="select" label="Choose vertical detector image bounds"> - <option value="full_range" selected="true">Use the full image range</option> - <option value="enter_range">Manually enter the image range</option> - </param> - <when value="full_range"/> - <when value="enter_range"> - <param name="low" type="integer" value="-1" optional="false" label="Lower image range index"/> - <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index"/> - </when> - </conditional> - </inputs> - <outputs> - <data name="tool_config" format="yaml" label="Tool config" from_work_dir="reduce.yaml" hidden="false"/> - <collection name="tomo_reduce_plots" type="list" label="Data reduction images"> - <discover_datasets pattern="__name_and_ext__" directory="tomo_reduce_plots"/> - </collection> - <data name="output_file" format="nex" label="Reduced tomography data" from_work_dir="output.nex"/> - </outputs> - <help> - <![CDATA[ - usage: PROG [-h] [--config CONFIG] [--verbose] - -options: - -h, --help show this help message and exit - --config CONFIG Input configuration file - --verbose verbose output - - ]]> - </help> - <expand macro="citations"/> -</tool>
--- a/tomo/tomo_reduce.xml Tue May 02 15:07:28 2023 +0000 +++ b/tomo/tomo_reduce.xml Mon May 15 19:15:16 2023 +0000 @@ -8,7 +8,6 @@ <![CDATA[ mkdir tomo_reduce_plots; #if str($map.type_selector) == "yaml" - $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' && cp $input_file map.yaml && cat $__tool_directory__/$map.detector.type_selector $tool_config > reduce.yaml && #else
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tomo/tomo_reduce_old.xml Mon May 15 19:15:16 2023 +0000 @@ -0,0 +1,94 @@ +<tool id="CHAP_tomo_reduce" name="Tomo Reduce" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@"> + <description>Reduce tomography images</description> + <macros> + <import>tomo_macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"> + <![CDATA[ + mkdir tomo_reduce_plots; + #if str($map.type_selector) == "yaml" + $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' && + cp $input_file map.yaml && + cat $__tool_directory__/$map.detector.type_selector $tool_config > reduce.yaml && + #else + cp $input_file setup.nex && + cp $tool_config reduce.yaml && + #end if + CHAP --config + #if str($map.type_selector) == "yaml" + $__tool_directory__/pipeline_reduce_yaml.yaml + #else + $__tool_directory__/pipeline_reduce_nexus.yaml + #end if + ]]> + </command> + <configfiles> + <configfile name="tool_config"> + <![CDATA[#slurp +#echo 'img_x_bounds:' # +#if str($img_x_bounds.type_selector) == "full_range" +#echo '- -1' # +#echo '- -1' # +#else +#echo '- ' + str($img_x_bounds.low) # +#echo '- ' + str($img_x_bounds.upp) # +#end if + ]]> + </configfile> + </configfiles> + <inputs> + <conditional name="map"> + <param name="type_selector" type="select" display="radio" label="Choose map file type"> + <option value="yaml">YAML</option> + <option value="nexus">NeXus</option> + </param> + <when value="yaml"> + <param name="input_file" type="data" format="yaml" optional="false" label="Map config file"/> + <conditional name="detector"> + <param name="type_selector" type="select" display="radio" label="Choose detector prefix"> + <option value="andor2.yaml">andor2</option> + <option value="manta.yaml">manta</option> + <option value="retiga.yaml">retiga</option> + </param> + <when value="andor2.yaml"/> + <when value="manta.yaml"/> + <when value="retiga.yaml"/> + </conditional> + </when> + <when value="nexus"> + <param name="input_file" type="data" format="nex" optional="false" label="Tomography setup file"/> + </when> + </conditional> + <conditional name="img_x_bounds"> + <param name="type_selector" type="select" label="Choose vertical detector image bounds"> + <option value="full_range" selected="true">Use the full image range</option> + <option value="enter_range">Manually enter the image range</option> + </param> + <when value="full_range"/> + <when value="enter_range"> + <param name="low" type="integer" value="-1" optional="false" label="Lower image range index"/> + <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="tool_config" format="yaml" label="Tool config" from_work_dir="reduce.yaml" hidden="false"/> + <collection name="tomo_reduce_plots" type="list" label="Data reduction images"> + <discover_datasets pattern="__name_and_ext__" directory="tomo_reduce_plots"/> + </collection> + <data name="output_file" format="nex" label="Reduced tomography data" from_work_dir="output.nex"/> + </outputs> + <help> + <![CDATA[ + usage: PROG [-h] [--config CONFIG] [--verbose] + +options: + -h, --help show this help message and exit + --config CONFIG Input configuration file + --verbose verbose output + + ]]> + </help> + <expand macro="citations"/> +</tool>