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meme*: add non_commercial_use to command #4241

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Nov 27, 2021
Merged

meme*: add non_commercial_use to command #4241

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3 changes: 2 additions & 1 deletion tools/meme/dreme.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="meme_dreme" name="DREME" version="@WRAPPER_VERSION@.0">
<tool id="meme_dreme" name="DREME" version="@TOOL_VERSION@.0">
<description>- Discriminative Regular Expression Motif Elicitation</description>
<macros>
<import>macros.xml</import>
Expand All @@ -7,6 +7,7 @@
<requirement type="package" version="2.7">python</requirement>
</expand>
<command detect_errors="exit_code"><![CDATA[
@CHECK_NON_COMMERCIAL_USE@
dreme
-o ./dreme_out
-p '$pos_fasta_file'
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3 changes: 2 additions & 1 deletion tools/meme/fimo.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="meme_fimo" name="FIMO" version="@WRAPPER_VERSION@.0">
<tool id="meme_fimo" name="FIMO" version="@TOOL_VERSION@.0">
<description>- Scan a set of sequences for motifs</description>
<xrefs>
<xref type="bio.tools">meme_fimo</xref>
Expand All @@ -8,6 +8,7 @@
</macros>
<expand macro="requirements" />
<command detect_errors="exit_code"><![CDATA[
@CHECK_NON_COMMERCIAL_USE@
fimo
-o ./out/
$scanrc
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8 changes: 7 additions & 1 deletion tools/meme/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,11 +1,17 @@
<?xml version='1.0' encoding='UTF-8'?>
<macros>
<token name="@WRAPPER_VERSION@">5.0.5</token>
<token name="@TOOL_VERSION@">5.0.5</token>
<xml name="requirements">
<requirements>
<requirement type="package" version="5.0.5">meme</requirement>
<yield/>
</requirements>
</xml>
<token name="@CHECK_NON_COMMERCIAL_USE@"><![CDATA[
#if not $non_commercial_use
>&2 echo "this tool is only available for non commercial use";
exit 1
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Should there be a ; at the end of the line here and below?

#end if
]]></token>
</macros>

3 changes: 2 additions & 1 deletion tools/meme/meme.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="meme_meme" name="MEME" version="@WRAPPER_VERSION@.0">
<tool id="meme_meme" name="MEME" version="@TOOL_VERSION@.0">
<description>- Multiple EM for Motif Elicitation</description>
<xrefs>
<xref type="bio.tools">meme_meme</xref>
Expand All @@ -8,6 +8,7 @@
</macros>
<expand macro="requirements" />
<command detect_errors="exit_code"><![CDATA[
@CHECK_NON_COMMERCIAL_USE@
export TMPDIR=\${TMPDIR:-.};

meme '$input1'
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3 changes: 2 additions & 1 deletion tools/meme/meme_psp_gen.xml
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Original file line number Diff line number Diff line change
@@ -1,10 +1,11 @@
<tool id="meme_psp_gen" name="MEME psp-gen" version="@WRAPPER_VERSION@.0">
<tool id="meme_psp_gen" name="MEME psp-gen" version="@TOOL_VERSION@.0">
<description>- perform discriminative motif discovery</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements" />
<command detect_errors="exit_code"><![CDATA[
@CHECK_NON_COMMERCIAL_USE@
ln -s '${primary_sequence}' meme_psp_input_pos.fa &&
ln -s '${control_sequence}' meme_psp_input_neg.fa &&
psp-gen
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8 changes: 7 additions & 1 deletion tools/meme_chip/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,11 +1,17 @@
<?xml version='1.0' encoding='UTF-8'?>
<macros>
<token name="@WRAPPER_VERSION@">4.11.2</token>
<token name="@TOOL_VERSION@">4.11.2</token>
<xml name="requirements">
<requirements>
<requirement type="package" version="1.3.23">graphicsmagick</requirement>
<requirement type="package" version="4.11.2">meme</requirement>
</requirements>
</xml>
<token name="@CHECK_NON_COMMERCIAL_USE@"><![CDATA[
#if not $non_commercial_use
>&2 echo "this tool is only available for non commercial use";
exit 1
#end if
]]></token>
</macros>

3 changes: 2 additions & 1 deletion tools/meme_chip/meme_chip.xml
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@@ -1,11 +1,12 @@
<tool id="meme_chip" name="MEME-ChIP" version="@WRAPPER_VERSION@+galaxy1">
<tool id="meme_chip" name="MEME-ChIP" version="@TOOL_VERSION@+galaxy1">
<description>- motif discovery, enrichment analysis and clustering on large nucleotide datasets</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements" />
<code file="get_meme_motif_databases.py" />
<command detect_errors="exit_code"><![CDATA[
@CHECK_NON_COMMERCIAL_USE@
#import os
#set primary_output = $os.path.join($output.files_path, "index.html")
meme-chip '$input'
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