annotate split_file_to_collection.xml @ 4:0850f2dfba13 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 872590086696cfbc248519507ecb9063926297ad"

<tool id="split_file_to_collection" name="Split file" version="0.3.0">
    <description>to dataset collection</description>
    <macros>
        <xml name="regex_sanitizer">
            <sanitizer>
                <valid>
                    <add preset="string.printable"/>
                    <remove value="&#92;" />
                    <remove value="&apos;" />
                </valid>
                <mapping initial="none">
                    <add source="&#92;" target="__backslash__" />
                    <add source="&apos;" target="__sq__"/>
                </mapping>
            </sanitizer>
        </xml>
        <xml name="numnew_fname">
            <conditional name="select_mode">
                <param name="mode" type="select" label="Specify number of output files or number of records per file?" help="Specify the number of records ('chunk size') to place in each file. The 'Number of new files' parameter will be ignored.">
                    <option value="chunk">Number of records per file ('chunk mode')</option>
                    <option value="numnew">Number of output files</option>
                </param>
                <when value="chunk">
                    <param name="chunksize" type="integer" label="Chunk size" min="1" value="1" help="Number of records per output file."/>
                </when>
                <when value="numnew">
                    <param name="numnew" type="integer" label="Number of new files" min="1" value="1"/>
                </when>
            </conditional>
            <param name="newfilenames" type="text" label="Base name for new files in collection"
                help="This will increment automatically - if input is 'file', then output is 'file0', 'file1', etc." value="split_file"/>
            <conditional name="select_allocate">
                <param name="allocate" type="select" label="Method to allocate records to new files" help="See the information section for a diagram">
                    <option value="random">At random</option>
                    <option value="batch">Maintain record order</option>
                    <option value="byrow" selected="true">Alternate output files</option>
                </param>
                <when value="random">
                    <param name="seed" type="integer" label="Random number seed" help="For reproducibility, set this to some arbitrary integer (e.g. '1010')" value="1010"/>
                </when>
                <when value="batch">
                </when>
                <when value="byrow">
                </when>
            </conditional>
        </xml>
    </macros>
    <requirements>
        <requirement type="package" version="3.5">python</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        mkdir ./out &&
        python '$__tool_directory__/split_file_to_collection.py'
            --out ./out
            --in '$split_parms.input'
            --ftype '$split_parms.select_ftype'
            #if $split_parms.select_ftype == "tabular":
                --top '$split_parms.top'
                --by '$split_parms.split_by.select_split_by'
                #if $split_parms.split_by.select_split_by == "col":
                    --id_column '$split_parms.split_by.id_col'
                    --match '$split_parms.split_by.match_regex'
                    --sub '$split_parms.split_by.sub_regex'
                #else
                    #if $split_parms.split_by.select_mode.mode == "numnew":
                        --numnew '$split_parms.split_by.select_mode.numnew'
                    #else
                        --chunksize $split_parms.split_by.select_mode.chunksize
                    #end if
                    #if $split_parms.split_by.select_allocate.allocate == "random":
                        --rand
                        --seed '$split_parms.split_by.rand.seed'
                    #end if
                    #if $split_parms.split_by.select_allocate.allocate == "batch":
                        --batch
                    #end if
                #end if
            #else
                #if $split_parms.select_ftype == "generic"
                    --generic_re '$split_parms.generic_regex'
                    #if $split_parms.split_after == 'true':
                        --split_after
                    #end if
                #end if
                #if $split_parms.select_mode.mode == "numnew":
                    --numnew '$split_parms.select_mode.numnew'
                #else
                    --chunksize $split_parms.select_mode.chunksize
                #end if
                #if $split_parms.select_allocate.allocate == "random":
                    --rand
                    --seed '$split_parms.select_allocate.seed'
                #end if
                #if $split_parms.select_allocate.allocate == "batch":
                    --batch
                #end if
            #end if
        #if ($split_parms.select_ftype == "tabular" and $split_parms.split_by.select_split_by == "row"):
             --file_names '$split_parms.split_by.newfilenames'
             --file_ext '$split_parms.select_ftype'
        #end if
        #if $split_parms.select_ftype != "tabular":
            --file_names '$split_parms.newfilenames'
            #if $split_parms.select_ftype == "generic"
                --file_ext '$split_parms.input.ext'
            #else
                --file_ext '$split_parms.select_ftype'
            #end if
        #end if
    ]]></command>
    <inputs>
        <conditional name="split_parms">
            <param name="select_ftype" type="select" label="Select the file type to split">
                <option value="mgf">MGF</option>
                <option value="fastq">FASTQ</option>
                <option value="tabular">Tabular</option>
                <option value="fasta">FASTA</option>
                <option value="sdf">SD-files</option>
                <option value="txt">Text files</option>
                <option value="generic">Generic</option>
            </param>
            <when value="tabular">
                <param name="input" type="data" format="tabular" label="Tabular file to split"/>
                <param name="top" type="integer" value="0" min="0" label="Number of header lines to transfer to new files"/>
                <conditional name="split_by">
                    <param name="select_split_by" type="select" label="Split by row or by a column?">
                        <option value="row">By row</option>
                        <option value="col">By column</option>
                    </param>
                    <when value="col">
                        <param name="id_col" type="data_column" label="Column to split on" data_ref="input"/>
                        <param name="match_regex" type="text" label="Regex to match contents of id column" value="(.*)">
                            <expand macro="regex_sanitizer"/>
                        </param>
                        <param name="sub_regex" type="text" label="Pattern to replace match with" value="\1">
                            <expand macro="regex_sanitizer"/>
                        </param>
                    </when>
                    <when value="row">
                        <expand macro="numnew_fname"/>
                    </when>
                </conditional>
            </when>
            <when value="mgf">
                <param name="input" type="data" format="mgf" label="MGF file to split"/>
                <expand macro="numnew_fname"/>
            </when>
            <when value="fastq">
                <param name="input" type="data" format="fastq" label="FASTQ file to split"/>
                <expand macro="numnew_fname"/>
            </when>
            <when value="fasta">
                <param name="input" type="data" format="fasta" label="FASTA file to split"/>
                <expand macro="numnew_fname"/>
            </when>
            <when value="sdf">
                <param name="input" type="data" format="sdf" label="SD-file to split"/>
                <expand macro="numnew_fname"/>
            </when>
            <when value="txt">
                <param name="input" type="data" format="txt" label="Text file to split"/>
                <expand macro="numnew_fname"/>
            </when>
            <when value="generic">
                <param name="input" type="data" format="txt" label="File to split"/>
                <param name="generic_regex" type="text" label="Regex to match record separator" value="^.*">
                    <expand macro="regex_sanitizer"/>
                </param>
                <expand macro="numnew_fname"/>
                <param name="split_after" type="select" value="false" label="Split records before or after the separator?" help="If before, the separator will appear at the start of each record; if after, at the end">
                    <option value="false" selected="true">Before</option>
                    <option value="true">After</option>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <collection name="list_output_tab" type="list" label="${tool.name} on ${on_string}">
            <discover_datasets pattern="__name__" directory="out" visible="false" format="tabular"/>
            <filter>split_parms['select_ftype'] == "tabular"</filter>
        </collection>
        <collection name="list_output_mgf" type="list" label="${tool.name} on ${on_string}">
            <discover_datasets pattern="__name__" directory="out" visible="false" format="mgf"/>
            <filter>split_parms['select_ftype'] == "mgf"</filter>
        </collection>
        <collection name="list_output_fasta" type="list" label="${tool.name} on ${on_string}">
            <discover_datasets pattern="__name__" directory="out" visible="false" format="fasta"/>
            <filter>split_parms['select_ftype'] == "fasta"</filter>
        </collection>
        <collection name="list_output_fastq" type="list" label="${tool.name} on ${on_string}">
            <discover_datasets pattern="__name__" directory="out" visible="false" format="fastq"/>
            <filter>split_parms['select_ftype'] == "fastq"</filter>
        </collection>
        <collection name="list_output_sdf" type="list" label="${tool.name} on ${on_string}">
            <discover_datasets pattern="__name__" directory="out" visible="false" format="sdf"/>
            <filter>split_parms['select_ftype'] == "sdf"</filter>
        </collection>
        <collection name="list_output_txt" type="list" label="${tool.name} on ${on_string}">
            <discover_datasets pattern="__name__" directory="out" visible="false" format="txt"/>
            <filter>split_parms['select_ftype'] == "txt"</filter>
        </collection>
        <collection name="list_output_generic" type="list" label="${tool.name} on ${on_string}">
            <discover_datasets pattern="__name_and_ext__" directory="out" visible="false"/>
            <filter>split_parms['select_ftype'] == "generic"</filter>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input" value="test.tabular" ftype="tabular"/>
            <param name="select_ftype" value="tabular"/>
            <param name="select_split_by" value="col"/>
            <param name="id_col" value="1"/>
            <param name="match_regex" value="(.*)\.mgf"/>
            <param name="sub_regex" value="\1.tab"/>
            <param name="top" value="2"/>
            <output_collection name="list_output_tab" type="list">
                <element name="foo.tab"  file="foo.tab" ftype="tabular"/>
                <element name="foo2.tab" file="foo2.tab" ftype="tabular"/>
                <element name="foo3.tab" file="foo3.tab" ftype="tabular"/>
            </output_collection>
        </test>
        <test>
            <param name="input" value="test.tabular" ftype="tabular"/>
            <param name="select_ftype" value="tabular"/>
            <param name="select_split_by" value="row"/>
            <param name="top" value="2"/>
            <param name="mode" value="numnew"/>
            <param name="numnew" value="2"/>
            <param name="newfilenames" value="test"/>
            <output_collection name="list_output_tab" type="list">
                <element name="test_000000.tabular" file="test_0.tabular" ftype="tabular"/>
                <element name="test_000001.tabular" file="test_1.tabular" ftype="tabular"/>
            </output_collection>
        </test>
        <test>
            <param name="input" value="test.tabular" ftype="tabular"/>
            <param name="select_ftype" value="tabular"/>
            <param name="select_split_by" value="row"/>
            <param name="top" value="2"/>
            <param name="mode" value="numnew"/>
            <param name="numnew" value="2"/>
            <param name="newfilenames" value="batch_tab"/>
            <param name="allocate" value="batch"/>
            <output_collection name="list_output_tab" type="list">
                <element name="batch_tab_000000.tabular" file="batch_tab_0.tabular" ftype="tabular"/>
                <element name="batch_tab_000001.tabular" file="batch_tab_1.tabular" ftype="tabular"/>
            </output_collection>
        </test>
        <test>
            <param name="input" value="test.tabular" ftype="tabular"/>
            <param name="select_ftype" value="tabular"/>
            <param name="select_split_by" value="row"/>
            <param name="top" value="2"/>
            <param name="mode" value="chunk"/>
            <param name="chunksize" value="2"/>
            <param name="newfilenames" value="batch_tab"/>
            <param name="allocate" value="batch"/>
            <output_collection name="list_output_tab" type="list">
                <element name="batch_tab_000000.tabular" file="batch_tab_0.tabular" ftype="tabular"/>
                <element name="batch_tab_000001.tabular" file="batch_tab_1.tabular" ftype="tabular"/>
            </output_collection>
        </test>
        <test>
            <param name="select_ftype" value="txt"/>
            <param name="input" value="karyotype.txt" ftype="txt"/>
            <param name="mode" value="numnew"/>
            <param name="numnew" value="24"/>
            <param name="newfilenames" value="chr"/>
            <param name="allocate" value="batch"/>

            <output_collection name="list_output_txt" type="list">
                <element name="chr_000000.txt" file="chr_000000.txt" ftype="txt"/>
                <element name="chr_000001.txt" file="chr_000001.txt" ftype="txt"/>
                <element name="chr_000002.txt" file="chr_000002.txt" ftype="txt"/>
                <element name="chr_000003.txt" file="chr_000003.txt" ftype="txt"/>
                <element name="chr_000004.txt" file="chr_000004.txt" ftype="txt"/>
                <element name="chr_000005.txt" file="chr_000005.txt" ftype="txt"/>
                <element name="chr_000006.txt" file="chr_000006.txt" ftype="txt"/>
                <element name="chr_000007.txt" file="chr_000007.txt" ftype="txt"/>
                <element name="chr_000008.txt" file="chr_000008.txt" ftype="txt"/>
                <element name="chr_000009.txt" file="chr_000009.txt" ftype="txt"/>
                <element name="chr_000010.txt" file="chr_000010.txt" ftype="txt"/>
                <element name="chr_000011.txt" file="chr_000011.txt" ftype="txt"/>
                <element name="chr_000012.txt" file="chr_000012.txt" ftype="txt"/>
                <element name="chr_000013.txt" file="chr_000013.txt" ftype="txt"/>
                <element name="chr_000014.txt" file="chr_000014.txt" ftype="txt"/>
                <element name="chr_000015.txt" file="chr_000015.txt" ftype="txt"/>
                <element name="chr_000016.txt" file="chr_000016.txt" ftype="txt"/>
                <element name="chr_000017.txt" file="chr_000017.txt" ftype="txt"/>
                <element name="chr_000018.txt" file="chr_000018.txt" ftype="txt"/>
                <element name="chr_000019.txt" file="chr_000019.txt" ftype="txt"/>
                <element name="chr_000020.txt" file="chr_000020.txt" ftype="txt"/>
                <element name="chr_000021.txt" file="chr_000021.txt" ftype="txt"/>
                <element name="chr_000022.txt" file="chr_000022.txt" ftype="txt"/>
                <element name="chr_000023.txt" file="chr_000023.txt" ftype="txt"/>
            </output_collection>
        </test>
        <test>
            <param name="input" value="psm.tabular" ftype="tabular"/>
            <param name="select_ftype" value="tabular"/>
            <param name="select_split_by" value="col"/>
            <param name="id_col" value="10"/>
            <param name="match_regex" value="(.*)\.mgf"/>
            <param name="sub_regex" value="\1.tab"/>
            <param name="top" value="1"/>
            <output_collection name="list_output_tab" type="list">
                <element name="file1.tab" file="file1.tab" ftype="tabular"/>
                <element name="file2.tab" file="file2.tab" ftype="tabular"/>
                <element name="file3.tab" file="file3.tab" ftype="tabular"/>
                <element name="file4.tab" file="file4.tab" ftype="tabular"/>
            </output_collection>
        </test>
        <test>
            <param name="input" value="demo758Dacentroid.mgf" ftype="mgf"/>
            <param name="select_ftype" value="mgf"/>
            <param name="mode" value="numnew"/>
            <param name="numnew" value="3"/>
            <param name="newfilenames" value="demo"/>
            <output_collection name="list_output_mgf" type="list">
                <element name="demo_000000.mgf" file="demo_0.mgf" ftype="mgf"/>
                <element name="demo_000001.mgf" file="demo_1.mgf" ftype="mgf"/>
                <element name="demo_000002.mgf" file="demo_2.mgf" ftype="mgf"/>
            </output_collection>
        </test>
        <test>
            <param name="input" value="test.fasta" ftype="fasta"/>
            <param name="select_ftype" value="fasta"/>
            <param name="mode" value="numnew"/>
            <param name="numnew" value="2"/>
            <param name="newfilenames" value="test"/>
            <output_collection name="list_output_fasta" type="list">
                <element name="test_000000.fasta" file="test_0.fasta" ftype="fasta"/>
                <element name="test_000001.fasta" file="test_1.fasta" ftype="fasta"/>
            </output_collection>
        </test>
        <test>
            <param name="input" value="test.fasta" ftype="fasta"/>
            <param name="select_ftype" value="fasta"/>
            <param name="mode" value="chunk"/>
            <param name="chunksize" value="3"/>
            <param name="newfilenames" value="test"/>
            <output_collection name="list_output_fasta" type="list">
                <element name="test_000000.fasta" file="test_0.fasta" ftype="fasta"/>
                <element name="test_000001.fasta" file="test_1.fasta" ftype="fasta"/>
            </output_collection>
        </test>
        <test>
            <param name="input" value="test.fastq" ftype="fastq"/>
            <param name="select_ftype" value="fastq"/>
            <param name="mode" value="numnew"/>
            <param name="numnew" value="2"/>
            <param name="newfilenames" value="test"/>
            <output_collection name="list_output_fastq" type="list">
                <element name="test_000000.fastq" file="test_0.fastq" ftype="fastq"/>
                <element name="test_000001.fastq" file="test_1.fastq" ftype="fastq"/>
            </output_collection>
        </test>
        <test>
            <param name="input" value="test.fasta" ftype="fasta"/>
            <param name="select_ftype" value="fasta"/>
            <param name="mode" value="numnew"/>
            <param name="numnew" value="2"/>
            <param name="newfilenames" value="rand"/>
            <param name="allocate" value="random"/>
            <param name="seed" value="1010"/>
            <output_collection name="list_output_fasta" type="list">
                <element name="rand_000000.fasta" file="rand_0.fasta" ftype="fasta"/>
                <element name="rand_000001.fasta" file="rand_1.fasta" ftype="fasta"/>
            </output_collection>
        </test>
        <test>
            <param name="input" value="test.fasta" ftype="fasta"/>
            <param name="select_ftype" value="fasta"/>
            <param name="mode" value="numnew"/>
            <param name="numnew" value="2"/>
            <param name="newfilenames" value="fasta_batch"/>
            <param name="allocate" value="batch"/>
            <output_collection name="list_output_fasta" type="list">
                <element name="fasta_batch_000000.fasta" file="fasta_batch_0.fasta" ftype="fasta"/>
                <element name="fasta_batch_000001.fasta" file="fasta_batch_1.fasta" ftype="fasta"/>
            </output_collection>
        </test>
        <test>
            <param name="input" value="test.tabular" ftype="txt"/>
            <param name="select_ftype" value="txt"/>
            <param name="mode" value="numnew"/>
            <param name="numnew" value="2"/>
            <param name="newfilenames" value="test"/>
            <output_collection name="list_output_txt" type="list">
                <element name="test_000000.txt" file="test_0.tabular" ftype="txt" lines_diff="1"/>
                <element name="test_000001.txt" file="test_1.tabular" ftype="txt" lines_diff="1"/>
            </output_collection>
        </test>
        <test>
            <param name="input" value="test.tabular" ftype="txt"/>
            <param name="select_ftype" value="generic"/>
            <param name="generic_regex" value="^.*"/>
            <param name="mode" value="numnew"/>
            <param name="numnew" value="2"/>
            <param name="newfilenames" value="test"/>
            <output_collection name="list_output_generic" type="list">
                <element name="test_000000" file="test_0.tabular" ftype="txt" lines_diff="1"/>
                <element name="test_000001" file="test_1.tabular" ftype="txt" lines_diff="1"/>
            </output_collection>
        </test>
        <test>
            <param name="input" value="test.fasta" ftype="fasta"/>
            <param name="select_ftype" value="generic"/>
            <param name="generic_regex" value="^>.*"/>
            <param name="mode" value="numnew"/>
            <param name="numnew" value="2"/>
            <param name="newfilenames" value="rand"/>
            <param name="allocate" value="random"/>
            <param name="seed" value="1010"/>
            <output_collection name="list_output_generic" type="list">
                <element name="rand_000000" file="rand_0.fasta" ftype="fasta"/>
                <element name="rand_000001" file="rand_1.fasta" ftype="fasta"/>
            </output_collection>
        </test>
        <test>
            <param name="input" value="3_molecules.sdf" ftype="sdf"/>
            <param name="select_ftype" value="sdf"/>
            <param name="mode" value="numnew"/>
            <param name="numnew" value="10"/>
            <param name="newfilenames" value="mol"/>
            <param name="allocate" value="batch"/>
            <output_collection name="list_output_sdf" type="list">
                <element name="mol_000000.sdf" file="mol_0.sdf" ftype="sdf"/>
                <element name="mol_000001.sdf" file="mol_1.sdf" ftype="sdf"/>
                <element name="mol_000002.sdf" file="mol_2.sdf" ftype="sdf"/>
            </output_collection>
        </test>
        <test>
            <param name="input" value="3_molecules.sdf" ftype="sdf"/>
            <param name="select_ftype" value="sdf"/>
            <param name="mode" value="chunk"/>
            <param name="chunksize" value="1"/>
            <param name="newfilenames" value="mol"/>
            <param name="allocate" value="batch"/>
            <output_collection name="list_output_sdf" type="list">
                <element name="mol_000000.sdf" file="mol_0.sdf" ftype="sdf"/>
                <element name="mol_000001.sdf" file="mol_1.sdf" ftype="sdf"/>
                <element name="mol_000002.sdf" file="mol_2.sdf" ftype="sdf"/>
            </output_collection>
        </test>
        <test>
            <param name="input" value="test.fasta" ftype="fasta"/>
            <param name="select_ftype" value="generic"/>
            <param name="generic_regex" value="^>.*"/>
            <param name="split_after" value="true"/>
            <param name="mode" value="numnew"/>
            <param name="numnew" value="2"/>
            <param name="newfilenames" value="rand"/>
            <param name="allocate" value="random"/>
            <param name="seed" value="1010"/>
            <output_collection name="list_output_generic" type="list">
                <element name="rand_000001" file="split_after.fasta" ftype="fasta"/>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
**Split file into a dataset collection**

This tool splits a data set consisting of records into multiple data sets within a collection.
A record can be for instance simply a line, a FASTA sequence (header + sequence), a FASTQ sequence
(headers + sequence + qualities), etc. The important property is that the beginning of a new record
can be specified by a regular expression, e.g. ".*" for lines, ">.*" for FASTA, or "@.*" for FASTQ.
The tool has presets for text, tabular data sets (which are split by line), FASTA, FASTQ, SDF and MGF.
For other data types the text delimiting records can be specified manually using the generic splitter. 
If the generic splitter is used, an option is also available to split records either before or after the
separator. If a preset filetype is used, this is selected automatically (after for SDF, before for all
others).

If splitting by line (or by some other item, like a FASTA entry or an MGF record), the splitting can be either done alternatingly, in original record order, or at random.

If t records are to be distributed to n new data sets, then the i-th record goes to data set

* floor(i / t * n) (for batch),
* i % n (for alternating), or
* a random data set

For instance, t=5 records are distributed as follows on n=2 data sets

= === === ====
i bat alt rand
= === === ====
0 0   0   0
1 0   1   1
2 0   0   1
3 1   1   0
4 1   0   0
= === === ====

If the five records are distributed on n=3 data sets:

= === === ====
i bat alt rand
= === === ====
0 0   0   0
1 0   1   1
2 1   2   2
3 1   0   0
4 2   1   1
= === === ====

Note that there are no guarantees when splitting at random that every result file will be non-empty, so downstream tools should be able to gracefully handle empty files.

If a tabular file is used as input, you may choose to split by line or by column. If split by column, a new file is created for each unique value in the column.
In addition, (Python) regular expressions may be used to transform the value in the column to a new value. Caution should be used with this feature, as it could transform all values to the same value, or other unexpected behavior.
The default regular expression uses each value in the column without modifying it.

Two modes are available for the tool. For the main mode, the number of output files is selected. In this case, records are shared out between this number of files. Alternatively, 'chunking mode' can be selected, which puts a fixed number of records (the 'chunk size') into each output file.

    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubsplit,
  author = {Easterly, Caleb},
  year = {2018},
  title = {A Galaxy tool for splitting a file into a collection},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/bgruening/galaxytools/tools/text_processing/split_file_to_collection},
}</citation>
    </citations>
</tool>