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80 lines
2.4 KiB
XML
80 lines
2.4 KiB
XML
<tool id="Show beginning1" name="Select first" version="1.0.2" profile="20.05">
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<description>lines from a dataset</description>
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<edam_operations>
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<edam_operation>operation_3695</edam_operation>
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</edam_operations>
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<requirements>
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<requirement type="package" version="8.31">coreutils</requirement>
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</requirements>
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<command><![CDATA[
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#if $header
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#set $n = int($lineNum) + 1
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#else
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#set $n = $lineNum
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#end if
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head -n $n '$input' > '$out_file1'
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]]></command>
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<inputs>
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<param name="lineNum" type="integer" value="10" min="1" label="Select first" help="lines"/>
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<param name="input" type="data" format="txt" label="from"/>
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<param name="header" type="boolean" label="Dataset has a header" help="if checked the header is kept and is not counted as a kept line"/>
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</inputs>
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<outputs>
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<data name="out_file1" format_source="input" metadata_source="input"/>
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</outputs>
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<tests>
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<test>
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<param name="lineNum" value="10"/>
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<param name="input" value="1.bed"/>
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<output name="out_file1" file="eq-showbeginning.dat">
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<assert_contents>
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<not_has_text text="CCDS9526.1_cds_0_0_chr13_112381695_f"/>
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<has_n_lines n="10"/>
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</assert_contents>
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</output>
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</test>
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<test>
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<param name="lineNum" value="1"/>
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<param name="input" value="GRCm38mm10_chr5_34761740-34912521.fa"/>
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<output name="out_file1">
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<assert_contents>
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<has_n_lines n="1"/>
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</assert_contents>
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</output>
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</test>
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<test>
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<param name="lineNum" value="10"/>
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<param name="input" value="1.bed"/>
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<param name="header" value="true"/>
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<output name="out_file1">
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<assert_contents>
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<has_text text="CCDS9526.1_cds_0_0_chr13_112381695_f"/>
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<has_n_lines n="11"/>
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</assert_contents>
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</output>
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</test>
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</tests>
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<help>
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**What it does**
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This tool outputs specified number of lines from the **beginning** of a dataset
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-----
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**Example**
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Selecting 2 lines from this::
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chr7 56632 56652 D17003_CTCF_R6 310 +
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chr7 56736 56756 D17003_CTCF_R7 354 +
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chr7 56761 56781 D17003_CTCF_R4 220 +
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chr7 56772 56792 D17003_CTCF_R7 372 +
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chr7 56775 56795 D17003_CTCF_R4 207 +
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will produce::
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chr7 56632 56652 D17003_CTCF_R6 310 +
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chr7 56736 56756 D17003_CTCF_R7 354 +
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</help>
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</tool>
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