Mercurial > repos > iuc > ucsc_mafaddirows

annotate mafAddIRows.xml @ 0:1e64bb6893b2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
author iuc
date Thu, 05 Jun 2025 19:23:48 +0000
parents
children 76f19f4cb5e6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
iuc
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1 <tool id="ucsc_mafaddirows" name="mafAddIRows" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2" license="MIT">
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
iuc
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2 <description>Add i rows to a MAF file</description>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
iuc
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3 <macros>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
iuc
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4 <token name="@TOOL_VERSION@">469</token>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
iuc
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5 <token name="@VERSION_SUFFIX@">0</token>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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6 </macros>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
iuc
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7 <requirements>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
iuc
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8 <requirement type="package" version="@TOOL_VERSION@">ucsc-mafaddirows</requirement>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
iuc
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9 </requirements>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
iuc
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10 <command detect_errors="exit_code"><![CDATA[
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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11 mafAddIRows
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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12 $input_maf
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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13 $twoBitFile
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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14 $output_maf
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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15 #if $nBeds
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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16 #import re
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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17 #for $bed in $nBeds:
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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18 #set identifier = re.sub('[^\s\w\-\\.]','_',str($bed.element_identifier))
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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19 && ln -s '$bed' '$identifier' &&
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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20 echo '$identifier' >> 'bed.txt'
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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21 #end for
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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22 -nBeds='bed.txt'
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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23 #end if
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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24 $addN
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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25 $addDash
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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26 ]]></command>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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27 <inputs>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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28 <param name="input_maf" type="data" format="maf" label="Input MAF file" help="MAF file with a single target sequence"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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29 <param name="twoBitFile" type="data" format="twobit" label="TwoBit reference file" help="TwoBit file for the reference genome"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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30 <param name="nBeds" type="data" format="bed" optional="true" multiple="true" label="List of BED files" help="One BED file per species with N locations"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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31 <param name="addN" type="boolean" truevalue="-addN" falsevalue="" label="Add rows of N's" help="Add rows of N's into MAF blocks instead of annotating them"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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32 <param name="addDash" type="boolean" truevalue="-addDash" falsevalue="" label="Add rows of -'s" help="Add rows of -'s into MAF blocks instead of annotating them"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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33 </inputs>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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34 <outputs>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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35 <data name="output_maf" format="maf" label="${tool.name} on ${on_string}: MAF output"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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36 </outputs>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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37 <tests>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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38 <!-- Test 1: Using -addN option -->
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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39 <test expect_num_outputs="1">
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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40 <param name="input_maf" value="mafIn.maf"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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41 <param name="twoBitFile" value="ref.2bit"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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42 <param name="addN" value="true"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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43 <param name="addDash" value="false"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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44 <output name="output_maf" ftype="maf">
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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45 <assert_contents>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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46 <has_n_lines n="8"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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47 <has_line line="i gorGor3.chr7 N 0 N 0"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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48 </assert_contents>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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49 </output>
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50 </test>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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51 <!-- Test 2: Using -addDash option -->
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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52 <test expect_num_outputs="1">
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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53 <param name="input_maf" value="mafIn.maf"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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54 <param name="twoBitFile" value="ref.2bit"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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55 <param name="addN" value="false"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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56 <param name="addDash" value="true"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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57 <output name="output_maf" ftype="maf">
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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58 <assert_contents>
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59 <has_n_lines n="8"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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60 <has_line line="i gorGor3.chr7 N 0 N 0"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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61 <has_line line="s panTro4.chr7 1000 20 + 159345973 ACGTAC-TAC-TACGTACGT"/>
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62 </assert_contents>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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63 </output>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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64 </test>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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65 <!-- Test 3: -nBeds option -->
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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66 <test expect_num_outputs="1">
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67 <param name="input_maf" value="mafIn.maf"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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68 <param name="twoBitFile" value="ref.2bit"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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69 <param name="nBeds" value="gorGor3.bed,hg38.bed,panTro4.bed"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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70 <param name="addN" value="true"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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71 <param name="addDash" value="false"/>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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72 <output name="output_maf" ftype="maf">
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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73 <assert_contents>
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74 <has_n_lines n="8"/>
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75 <has_line line="i gorGor3.chr7 N 0 N 0"/>
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76 </assert_contents>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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77 </output>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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78 </test>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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79 </tests>
1e64bb6893b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 06cd9c75a53dc14c476349a3c12d7428a5aa351c
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80 <help><![CDATA[
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81 **mafAddIRows**
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82
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83 This tool adds 'i' rows to a Multiple Alignment Format (MAF) file. It requires a MAF file with a single target sequence.
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84
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85 **Usage**
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86
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87 - **Input MAF file**: Provide a MAF file containing alignments with only one target sequence.
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88 - **TwoBit reference file**: Specify a TwoBit file for the reference genome.
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89 - **List of BED files** (optional): Provide BED files (one per species) specifying N locations.
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90 - **Add rows of N's**: Check to insert rows of N's into MAF blocks instead of annotating.
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91 - **Add rows of -'s**: Check to insert rows of -'s into MAF blocks instead of annotating.
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92
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93 **Output**
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94
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95 - A modified MAF file with added 'i' rows or annotations based on the provided options.
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96
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97 **Note**
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98
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99 - The input MAF file must contain only a single target sequence.
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100 - Use either `-addN` or `-addDash`, but not both, to modify the MAF blocks directly.
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101 ]]></help>
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102 <citations>
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103 <citation type="bibtex">
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104 @misc{mafAddIRows,
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105 title = {mafAddIRows: Add 'i' rows to a MAF file},
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106 author = {Kent UCSC},
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107 note = {Tool for adding 'i' rows to MAF files with a single target sequence}
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108 }
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109 </citation>
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110 </citations>
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111 <creator>
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112 <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12"/>
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113 <organization name="Galaxy Europe" url="https://galaxyproject.org/eu/"/>
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114 </creator>
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115 </tool>