Mercurial > repos > rjmw > dimspy_hdf5_to_txt
diff hdf5_to_txt.xml @ 1:6585fa639f7f draft default tip
planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
| author | rjmw |
|---|---|
| date | Wed, 30 May 2018 09:13:55 -0400 |
| parents | 067888b11880 |
| children |
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--- a/hdf5_to_txt.xml Tue Feb 27 13:59:08 2018 -0500 +++ b/hdf5_to_txt.xml Wed May 30 09:13:55 2018 -0400 @@ -4,18 +4,18 @@ <import>macros.xml</import> </macros> <expand macro="requirements" /> - <expand macro="stdio" /> - <command><![CDATA[ + <command detect_errors="exit_code"> + <![CDATA[ #if $input.object_type == "peak_lists" dimspy hdf5-pls-to-txt - --input "$input.hdf5_file_in" + --input '$input.hdf5_file_in' --output . --delimiter $delimiter #elif $input.object_type == "peak_matrix" #if $input.matrix_format == "standard" or $input.matrix_format == "standard_comprehensive" dimspy hdf5-pm-to-txt - --input "$input.hdf5_file_in" - --output "$matrix_file_out" + --input '$input.hdf5_file_in' + --output '$matrix_file_out' --delimiter $delimiter --attribute_name $input.matrix_attr --representation-samples $input.representation_samples @@ -25,15 +25,16 @@ #end if #if $input.matrix_format == "comprehensive" or $input.matrix_format == "standard_comprehensive" dimspy hdf5-pm-to-txt - --input "$input.hdf5_file_in" - --output "$matrix_comprehensive_file_out" + --input '$input.hdf5_file_in' + --output '$matrix_comprehensive_file_out' --delimiter $delimiter --comprehensive - --attribute_name $input.matrix_attr + --attribute_name '$input.matrix_attr' --representation-samples $input.representation_samples #end if #end if - ]]></command> + ]]> + </command> <inputs> <param name="delimiter" type="hidden" value="tab" argument="--delimiter"/> <conditional name="input">