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annotate macros.xml @ 0:5b44ef788111 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
author iuc
date Wed, 19 Sep 2018 08:21:27 -0400
parents
children 390fc279c3e5
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0
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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1 <macros>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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2 <xml name="requirements">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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3 <requirements>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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4 <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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5 <yield/>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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6 </requirements>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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7 </xml>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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8 <token name="@TOOL_VERSION@">1.9</token>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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9 <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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10 <token name="@PREPARE_IDX@"><![CDATA[
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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11 ##prepare input and indices
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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12 ln -s '$input' infile &&
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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13 #if $input.is_of_type('bam'):
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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14 #if str( $input.metadata.bam_index ) != "None":
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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15 ln -s '${input.metadata.bam_index}' infile.bai &&
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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16 #else:
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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17 samtools index infile infile.bai &&
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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18 #end if
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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19 #elif $input.is_of_type('cram'):
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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20 #if str( $input.metadata.cram_index ) != "None":
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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21 ln -s '${input.metadata.cram_index}' infile.crai &&
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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22 #else:
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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23 samtools index infile infile.crai &&
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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24 #end if
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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25 #end if
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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26 ]]></token>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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27 <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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28 ##prepare input and indices
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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29 #for $i, $bam in enumerate( $input_bams ):
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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30 ln -s '$bam' '${i}' &&
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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31 #if $bam.is_of_type('bam'):
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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32 #if str( $bam.metadata.bam_index ) != "None":
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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33 ln -s '${bam.metadata.bam_index}' '${i}.bai' &&
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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34 #else:
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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35 samtools index '${i}' '${i}.bai' &&
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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36 #end if
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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37 #elif $bam.is_of_type('cram'):
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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38 #if str( $bam.metadata.cram_index ) != "None":
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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39 ln -s '${bam.metadata.cram_index}' '${i}.crai' &&
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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40 #else:
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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41 samtools index '${i}' '${i}.crai' &&
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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42 #end if
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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43 #end if
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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44 #end for
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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45 ]]></token>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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46 <token name="@PREPARE_FASTA_IDX@"><![CDATA[
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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47 ##checks for reference data ($addref_cond.addref_select=="history" or =="cached")
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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48 ##and sets the -t/-T parameters accordingly:
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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49 ##- in case of history a symbolic link is used because samtools (view) will generate
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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50 ## the index which might not be possible in the directory containing the fasta file
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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51 ##- in case of cached the absolute path is used which allows to read the cram file
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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52 ## without specifying the reference
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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53 #if $addref_cond.addref_select == "history":
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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54 ln -s '${addref_cond.ref}' reference.fa &&
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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55 samtools faidx reference.fa &&
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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56 #set reffa=str($addref_cond.ref)
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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57 #set reffai="reference.fa.fai"
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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58 #elif $addref_cond.addref_select == "cached":
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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59 #set reffa=str($addref_cond.ref.fields.path)
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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60 #set reffai=str($addref_cond.ref.fields.path)
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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61 #else
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62 #set reffa=None
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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63 #set reffai=None
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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64 #end if
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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65 ]]></token>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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66 <token name="@ADDTHREADS@"><![CDATA[
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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67 ##compute the number of ADDITIONAL threads to be used by samtools (-@)
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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68 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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69 ]]></token>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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70 <xml name="flag_options">
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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71 <option value="1">read is paired</option>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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72 <option value="2">read is mapped in a proper pair</option>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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73 <option value="4">read is unmapped</option>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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74 <option value="8">mate is unmapped</option>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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75 <option value="16">read reverse strand</option>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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76 <option value="32">mate reverse strand</option>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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77 <option value="64">read is the first in a pair</option>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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78 <option value="128">read is the second in a pair</option>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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79 <option value="256">alignment or read is not primary</option>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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80 <option value="512">read fails platform/vendor quality checks</option>
5b44ef788111 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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81 <option value="1024">read is a PCR or optical duplicate</option>
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82 <option value="2048">supplementary alignment</option>
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83 </xml>
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84 <xml name="citations">
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85 <citations>
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86 <citation type="bibtex">
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87 @misc{SAM_def,
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88 title={Definition of SAM/BAM format},
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89 url = {https://samtools.github.io/hts-specs/},}
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90 </citation>
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91 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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92 <citation type="doi">10.1093/bioinformatics/btr076</citation>
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93 <citation type="doi">10.1093/bioinformatics/btr509</citation>
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94 <citation type="bibtex">
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95 @misc{Danecek_et_al,
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96 Author={Danecek, P., Schiffels, S., Durbin, R.},
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97 title={Multiallelic calling model in bcftools (-m)},
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98 url = {http://samtools.github.io/bcftools/call-m.pdf},}
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99 </citation>
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100 <citation type="bibtex">
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101 @misc{Durbin_VCQC,
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102 Author={Durbin, R.},
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103 title={Segregation based metric for variant call QC},
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104 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
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105 </citation>
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106 <citation type="bibtex">
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107 @misc{Li_SamMath,
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108 Author={Li, H.},
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109 title={Mathematical Notes on SAMtools Algorithms},
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110 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
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111 </citation>
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112 <citation type="bibtex">
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113 @misc{SamTools_github,
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114 title={SAMTools GitHub page},
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115 url = {https://github.com/samtools/samtools},}
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116 </citation>
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117 </citations>
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118 </xml>
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119 <xml name="version_command">
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120 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
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121 </xml>
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122 <xml name="stdio">
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123 <stdio>
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124 <exit_code range="1:" level="fatal" description="Error" />
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125 </stdio>
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126 </xml>
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127 </macros>