| Previous changeset 26:93595f42a04d (2023-08-02) Next changeset 28:ba970b24e48c (2023-08-02) |
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Commit message:
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty |
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modified:
extract_files_from_re_archive.xml |
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| diff -r 93595f42a04d -r eefed7a82001 extract_files_from_re_archive.xml --- a/extract_files_from_re_archive.xml Wed Aug 02 12:45:16 2023 +0000 +++ b/extract_files_from_re_archive.xml Wed Aug 02 12:59:29 2023 +0000 |
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| @@ -1,49 +1,68 @@ -<tool id="extract_var_files_from_re" name="Extract various files from RepeatExplorer2 archive" version="1.0.0.3"> - <command detect_errors="exit_code"> +<tool id="extract_var_files_from_re" + name="Extract various files from RepeatExplorer2 archive" version="1.0.0.3"> + <command detect_errors="exit_code"> + <![CDATA[ + + #for $sf in $file: - #if $sf == "CLUSTER_TABLE.csv" - unzip -p -j ${RepeatExplorer_archive} ${sf} > ${cluster_table} + mkdir -p tempdir + unzip ${RepeatExplorer_archive} ${sf} -d tempdir + find tempdir -type f -name "${sf}" -exec cat {} + > ${cluster_table} + rm -r tempdir ; #end if #if $sf == "COMPARATIVE_ANALYSIS_COUNTS.csv" - unzip -p -j ${RepeatExplorer_archive} ${sf} > ${comparative_analysis_count} + mkdir -p tempdir + unzip ${RepeatExplorer_archive} ${sf} -d tempdir + find tempdir -type f -name "${sf}" -exec cat {} + > ${comparative_analysis_count} + rm -r tempdir ; #end if #if $sf == "SUPERCLUSTER_TABLE.csv" - unzip -p -j ${RepeatExplorer_archive} ${sf} > ${supercluster_table} - ; + mkdir -p tempdir + unzip ${RepeatExplorer_archive} ${sf} -d tempdir + find tempdir -type f -name "${sf}" -exec cat {} + > ${supercluster_table} + rm -r tempdir #end if #end for +]]> - </command> - - <inputs> - <param name="RepeatExplorer_archive" label="Archive with RepeatExplorer2 results" type="data" format="zip"/> + </command> - <param name="file" type="select" label="select files you want to extract" multiple="true" optional="false"> - <option value="CLUSTER_TABLE.csv">CLUSTER_TABLE.csv</option> - <option value="COMPARATIVE_ANALYSIS_COUNTS.csv">COMPARATIVE_ANALYSIS_COUNTS.csv</option> - <option value="SUPERCLUSTER_TABLE.csv">SUPERCLUSTER_TABLE.csv</option> - </param> - </inputs> + <inputs> + <param name="RepeatExplorer_archive" label="Archive with RepeatExplorer2 results" + type="data" format="zip"/> - <outputs> - <data format="tabular" name="cluster_table" label="CLUSTER_TABLE.csv from ${RepeatExplorer_archive.hid}" > - <filter>"CLUSTER_TABLE.csv" in file</filter> - </data> - <data format="tabular" name="supercluster_table" label="SUPERCLUSTER_TABLE.csv from ${RepeatExplorer_archive.hid}"> - <filter>"SUPERCLUSTER_TABLE.csv" in file</filter> - </data> - <data format="tabular" name="comparative_analysis_count" label="COMPARATIVE_ANALYSIS_COUNTS.csv from ${RepeatExplorer_archive.hid}"> - <filter>"COMPARATIVE_ANALYSIS_COUNTS.csv" in file</filter> - </data> - </outputs> + <param name="file" type="select" label="select files you want to extract" + multiple="true" optional="false"> + <option value="CLUSTER_TABLE.csv">CLUSTER_TABLE.csv</option> + <option value="COMPARATIVE_ANALYSIS_COUNTS.csv"> + COMPARATIVE_ANALYSIS_COUNTS.csv + </option> + <option value="SUPERCLUSTER_TABLE.csv">SUPERCLUSTER_TABLE.csv</option> + </param> + </inputs> + + <outputs> + <data format="tabular" name="cluster_table" + label="CLUSTER_TABLE.csv from ${RepeatExplorer_archive.hid}"> + <filter>"CLUSTER_TABLE.csv" in file</filter> + </data> + <data format="tabular" name="supercluster_table" + label="SUPERCLUSTER_TABLE.csv from ${RepeatExplorer_archive.hid}"> + <filter>"SUPERCLUSTER_TABLE.csv" in file</filter> + </data> + <data format="tabular" name="comparative_analysis_count" + label="COMPARATIVE_ANALYSIS_COUNTS.csv from ${RepeatExplorer_archive.hid}"> + <filter>"COMPARATIVE_ANALYSIS_COUNTS.csv" in file</filter> + </data> + </outputs> </tool> |