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1 <tool id="gops_concat_1" name="Concatenate" version="1.0.1">
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2 <description>two datasets into one dataset</description>
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3 <requirements>
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4 <requirement type="package" version="0.7.1">bx-python</requirement>
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5 <requirement type="package" version="1.0.0">galaxy-ops</requirement>
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6 </requirements>
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7 <command interpreter="python">gops_concat.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} $sameformat</command>
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8 <inputs>
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9 <param format="interval" name="input1" type="data" help="First dataset">
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10 <label>Concatenate</label>
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11 </param>
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12 <param format="interval" name="input2" type="data" help="Second dataset">
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13 <label>with</label>
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14 </param>
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15 <param name="sameformat" type="boolean" truevalue="--sameformat" falsevalue="" label="Both datasets are same filetype?" checked="true" help="If unchecked Second dataset will be forced into format of First dataset">
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16 </param>
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17 </inputs>
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18 <outputs>
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19 <data format="input" name="output" metadata_source="input1" />
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20 </outputs>
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21 <code file="operation_filter.py"/>
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22 <tests>
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23 <test>
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24 <param name="input1" value="1.bed" />
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25 <param name="input2" value="2.bed" />
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26 <param name="sameformat" value="true" />
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27 <output name="output" file="gops_concat_out1.bed" />
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28 </test>
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29 <test>
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30 <param name="input1" value="1.bed" />
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31 <param name="input2" value="1.interval" />
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32 <param name="sameformat" value="false" />
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33 <output name="output" file="gops_concat_out2.bed" />
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34 </test>
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35 </tests>
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36 <help>
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37
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38 .. class:: infomark
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39
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40 **TIP:** If your dataset does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.
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41
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42 -----
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43
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44 **Screencasts!**
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45
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46 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
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47
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48 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
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49
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50 -----
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51
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52 **Syntax**
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53
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54 - **Both datasets are exactly the same filetype** will preserve all extra fields in both files. Leaving this unchecked will force the second dataset to use the same column assignments for chrom, start, end and strand, but will fill extra fields with a period(.). In both cases, the output fields are truncated or padded with fields of periods to maintain a truly tabular output.
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55
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56 -----
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57
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58 **Example**
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59
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60 .. image:: gops_concatenate.gif
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61
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62 </help>
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63 </tool> |
