Mercurial > repos > bgruening > text_processing
comparison multijoin.xml @ 4:56e80527c482 draft
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| author | bgruening |
|---|---|
| date | Wed, 07 Jan 2015 11:10:52 -0500 |
| parents | 7068d1548234 |
| children | 3f0e0d4c15a9 |
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| 3:7068d1548234 | 4:56e80527c482 |
|---|---|
| 1 <tool id="tp_multijoin'_tool" name="Multi-Join" version="0.1.1"> | 1 <tool id="tp_multijoin'_tool" name="Multi-Join" version="@BASE_VERSION@.0"> |
| 2 <description>(combine multiple files)</description> | 2 <description>(combine multiple files)</description> |
| 3 <command interpreter="perl">multijoin | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"> | |
| 7 <requirement type="package" version="5.18">perl</requirement> | |
| 8 <requirement type="package" version="1.0">text_processing_perl_packages</requirement> | |
| 9 </expand> | |
| 10 <command interpreter="perl"> | |
| 11 <![CDATA[ | |
| 12 multijoin | |
| 4 --key '$key_column' | 13 --key '$key_column' |
| 5 --values '$value_columns' | 14 --values '$value_columns' |
| 6 --filler '$filler' | 15 --filler '$filler' |
| 7 $ignore_dups | 16 $ignore_dups |
| 8 $output_header | 17 $output_header |
| 9 $input_header | 18 $input_header |
| 10 $first_filename | 19 $first_file |
| 11 #for $file in $files | 20 #for $file in $files: |
| 12 '$file.filename' | 21 '$file' |
| 13 #end for | 22 #end for |
| 14 > '$output' | 23 > '$outfile' |
| 15 </command> | 24 ]]> |
| 25 </command> | |
| 26 <inputs> | |
| 27 <param name="first_file" type="data" format="txt" label="File to join"/> | |
| 28 <param name="files" multiple="True" type="data" format="txt" label="add additional file" /> | |
| 16 | 29 |
| 17 <inputs> | 30 <param name="key_column" label="Common key column" type="integer" |
| 31 value="1" help="Usually gene-ID or other common value" /> | |
| 18 | 32 |
| 19 <param name="first_filename" label="File to join" type="data" format="txt" /> | 33 <param name="value_columns" label="Column with values to preserve" |
| 20 <repeat name="files" title="with" min="2"> | 34 type="data_column" data_ref="first_file" accept_default="true" multiple="True" display="checkboxes"/> |
| 21 <param name="filename" label="add additional file" type="data" format="txt" /> | |
| 22 </repeat> | |
| 23 | 35 |
| 24 <param name="key_column" label="Common key column" type="integer" | 36 <param name="output_header" type="boolean" checked="false" truevalue="--out-header" falsevalue="" label="Add header line to the output file" help="" /> |
| 25 value="1" help="Usually gene-ID or other common value" /> | 37 <param name="input_header" type="boolean" checked="false" truevalue="--in-header" falsevalue="" label="Input files contain a header line (as first line)" help="" /> |
| 26 | 38 <param name="ignore_dups" type="boolean" checked="false" truevalue="--ignore-dups" falsevalue="" label="Ignore duplicated keys" help="If not set, duplicated keys in the same file will cause an error." /> |
| 27 <param name="value_columns" label="Column with values to preserve" | 39 <param name="filler" type="text" size="20" value="0" label="Value to put in unpaired (empty) fields"> |
| 28 type="data_column" data_ref="first_filename" accept_default="true" multiple="True" display="checkboxes"/> | 40 <sanitizer> |
| 29 | 41 <valid initial="string.printable"> |
| 30 <param name="output_header" type="boolean" checked="false" truevalue="--out-header" falsevalue="" label="Add header line to the output file" help="" /> | 42 <remove value="'"/> |
| 31 <param name="input_header" type="boolean" checked="false" truevalue="--in-header" falsevalue="" label="Input files contain a header line (as first line)" help="" /> | 43 </valid> |
| 32 <param name="ignore_dups" type="boolean" checked="false" truevalue="--ignore-dups" falsevalue="" label="Ignore duplicated keys" help="If not set, duplicated keys in the same file will cause an error." /> | 44 </sanitizer> |
| 33 <param name="filler" type="text" size="20" value="0" label="Value to put in unpaired (empty) fields"> | 45 </param> |
| 34 <sanitizer> | 46 </inputs> |
| 35 <valid initial="string.printable"> | 47 <outputs> |
| 36 <remove value="'"/> | 48 <data name="outfile" format="first_file" metadata_source="first_file" /> |
| 37 </valid> | 49 </outputs> |
| 38 </sanitizer> | 50 <tests> |
| 39 </param> | 51 <test> |
| 40 | 52 <param name="first_file" value="multijoin1.txt" /> |
| 41 </inputs> | 53 <param name="files" value="multijoin2.txt,multijoin3.txt" /> |
| 42 <outputs> | 54 <param name="key_column" value="4" /> |
| 43 <data name="output" format="input" metadata_source="input" /> | 55 <param name="value_columns" value="c7,c8,c9" /> |
| 44 </outputs> | 56 <param name="output_header" value="True" /> |
| 45 | 57 <output name="outfile" file="multijoin_result1.txt" /> |
| 46 <help> | 58 </test> |
| 59 </tests> | |
| 60 <help> | |
| 61 <![CDATA[ | |
| 47 **What it does** | 62 **What it does** |
| 48 | 63 |
| 49 This tool joins multiple tabular files based on a common key column. | 64 This tool joins multiple tabular files based on a common key column. |
| 50 | 65 |
| 51 ----- | 66 ----- |
| 106 FBtr0111045 28 683 2138 0 0 0 17 714 2138 | 121 FBtr0111045 28 683 2138 0 0 0 17 714 2138 |
| 107 FBtr0111046 7 166 642 0 0 0 5 304 642 | 122 FBtr0111046 7 166 642 0 0 0 5 304 642 |
| 108 FBtr0300796 0 0 0 56 1296 14475 0 0 0 | 123 FBtr0300796 0 0 0 56 1296 14475 0 0 0 |
| 109 ... | 124 ... |
| 110 | 125 |
| 126 .. class:: infomark | |
| 111 | 127 |
| 112 # Input files need not be sorted. | 128 Input files need not be sorted. |
| 113 | 129 |
| 114 ----- | 130 @REFERENCES@ |
| 115 | 131 ]]> |
| 116 *multijoin* was written by A. Gordon (gordon at cshl dot edu) | 132 </help> |
| 117 | |
| 118 </help> | |
| 119 </tool> | 133 </tool> |