Mercurial > repos > iuc > ont_fast5_api_fast5_subset
view fast5_subset.xml @ 3:0defe443ea04 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api commit e83fdc3a33f17709196a0f5567fbec42f9f31922"
author | iuc |
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date | Sat, 23 Oct 2021 20:37:51 +0000 |
parents | 33a0ff1bb7df |
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<tool id="ont_fast5_api_fast5_subset" name="@TOOL_NAME@ Subset" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> <description>of multi read file(s)</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <!-- no specific version command for subcommand fast5_subset available --> <version_command><![CDATA[compress_fast5 -v]]></version_command> <command detect_errors="exit_code"><![CDATA[ ## initialize mkdir -p './data' && tar -xf '$input' -C './data' && ## run fast5_subset --recursive ## required --input './data' @SAVEPATH@ --read_id_list '$read_id_list' ## optional @COMPRESSION@ @BATCHSIZE@ @THREADS@ ## create tarball @TARBALL@ ]]></command> <inputs> <expand macro="input" argument="--input"/> <param argument="--read_id_list" type="data" format="txt,tabular" label="Select file with read IDs" help="Either containing 1 read_id per line or a tabular file with a column named read_id."/> <expand macro="batch_size"/> <expand macro="compression"> <option value="none" selected="true">None</option> <option value="vbz">VBZ</option> </expand> </inputs> <outputs> <expand macro="output"/> </outputs> <tests> <!-- #1 default --> <test expect_num_outputs="1"> <param name="input" value="multi.fast5.tar"/> <param name="read_id_list" value="list.txt"/> <output name="out_results"> <assert_contents> <has_size value="30720"/> </assert_contents> </output> </test> <!-- #2 --> <test expect_num_outputs="1"> <param name="input" value="multi.fast5.tar"/> <param name="read_id_list" value="list.txt"/> <param name="batch_size" value="2"/> <param name="compression" value="gzip"/> <output name="out_results"> <assert_contents> <has_size value="51200"/> </assert_contents> </output> </test> <!-- #3 --> <test expect_num_outputs="1"> <param name="input" value="multi.fast5.tar"/> <param name="read_id_list" value="list.txt"/> <param name="compression" value="vbz"/> <output name="out_results"> <assert_contents> <has_size value="40960"/> </assert_contents> </output> </test> <!-- #4 --> <test expect_num_outputs="1"> <param name="input" value="multi.fast5.tar"/> <param name="read_id_list" value="list.txt"/> <param name="compression" value="vbz_legacy_v0"/> <output name="out_results"> <assert_contents> <has_size value="40960"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** @WID@ *fast5_subset* extracts reads from multi read FAST5 file(s) based on a list of read IDs. **Input** Multi read file(s) in FAST5 format, that are stored in a flat TAR, and a list of read IDs that should be extracted. **Output** Multi read file(s) in FAST5 format containing a subset of the input file(s). The rseults are are stored in a flat TAR. .. class:: infomark **References** @REFERENCES@ ]]></help> <expand macro="citations"/> </tool>